We have the known,
$$I(z)=\int_0^z\ln\Gamma(t)~dt=\frac{z(1-z)}2+\frac z2\ln(2\pi)+z\ln\Gamma(z)-\ln G(z+1)$$ or alternatively, $$I(z)=\int_0^z\ln\Gamma(t)~dt= \frac{z(1-z)}{2}+\frac{z}{2}\ln(2\pi) -(1-z)\ln\Gamma(z) -\ln G(z)$$
since the Barnes G-function obeys $G(1+z)=\Gamma(z)\, G(z)$.
The Barnes G-function $G(z)$ is rather exotic (BarnesG(z) in WA syntax), and we may wonder if it can be expressed in terms of other special functions like polylogs or polygammas. It turns out for $z$ a unit fraction, one can do so for $z = 1,\frac12,\frac13,\frac14,\frac16$. Given the Clausen function $\operatorname{Cl}_2(z)$ and,
$$\begin{aligned} A \;&= \text{Glaisher–Kinkelin constant}\\ \operatorname{Cl}_2\left(\frac\pi2\right) &=\text{Catalan's constant}\\ \operatorname{Cl}_2\left(\frac\pi3\right) &=\text{Gieseking's constant} \end{aligned}$$
then,
$$\begin{aligned} \ln G\left(\frac11\right)\;&= \;0\\ \ln G\left(\frac12\right) &= -\frac32\ln A -\frac12\ln\Gamma\left(\frac12\right)+\frac1{24}\ln 2+\frac1{8}\\ \ln G\left(\frac13\right) &= -\frac43\ln A -\frac23\ln\Gamma\left(\frac13\right)-\frac{1}{6\pi}\operatorname{Cl}_2\left(\frac\pi3\right)+\frac1{72}\ln 3+\frac1{9}\\ \ln G\left(\frac14\right) &= -\frac98\ln A -\frac34\ln\Gamma\left(\frac14\right)-\frac{1}{4\pi}\operatorname{Cl}_2\left(\frac\pi2\right)+\frac3{32}\\ \ln G\left(\frac16\right) &= -\frac56\ln A -\frac56\ln\Gamma\left(\frac16\right)-\frac{1}{4\pi}\operatorname{Cl}_2\left(\frac\pi3\right)-\frac1{72}\ln 2-\frac1{144}\ln3+\frac5{72}\\ \end{aligned}$$
Q: Can we find a closed-form of the Barnes G-function $G(z)$, hence the log gamma integral $I(z)$, for other unit fraction $z \neq 1,\frac12,\frac13,\frac14,\frac16$?
Let's use integration by parts:
$$I(z)=\int_0^z\ln\Gamma(t)~dt=z \ln\Gamma(z)-\int_0^z t \psi(t) dt$$
$$\psi(t)=\log t-\frac{1}{2t}-2 \int_0^\infty \frac{udu}{(u^2+t^2)(e^{2 \pi u}-1)}$$
$$\int_0^z t \log t dt=\frac{z^2}{4} (2 \log z-1)$$
$$\frac{1}{2}\int_0^z dt=\frac{z}{2}$$
$$2 \int_0^z \frac{t dt}{u^2+t^2}=\log \left(1+ \frac{z^2}{u^2} \right)$$
Which gives us:
$$I(z)=z \ln\Gamma(z)+\frac{z^2}{4} (1-2 \log z)+\frac{z}{2}+\int_0^\infty \frac{udu}{e^{2 \pi u}-1} \log \left(1+ \frac{z^2}{u^2} \right)$$
Comparing with the expression from the OP, we have:
Let's concider the integral:
$$J(z)=\int_0^\infty \frac{udu}{e^{2 \pi u}-1} \log \left(1+ \frac{z^2}{u^2} \right)$$
Let's change the variable:
$$u=z v$$
$$J(z)=z^2 \int_0^\infty \frac{vdv}{e^{2 \pi z v}-1} \log \left(1+ \frac{1}{v^2} \right)$$
$$J(z)=z^2 \sum_{n=1}^\infty \int_0^\infty e^{-2 \pi n z v}v \log \left(1+ \frac{1}{v^2} \right) dv$$
We have:
$$z^2 \int_0^\infty e^{-2 \pi n z v}v \log \left(1+ v^2 \right) dv= \\ = \frac{1}{2 \pi^2 n^2} \left([2 \pi n z \cos (2 \pi n z)-\sin (2 \pi n z) ] \left(\operatorname{Si}(2 \pi n z)-\frac{\pi}{2} \right)- \\ -[2 \pi n z \sin (2 \pi n z)+\cos (2 \pi n z) ] \operatorname{Ci}(2 \pi n z)+1 \right)$$
$$2z^2 \int_0^\infty e^{-2 \pi n z v}v \log \left(v \right) dv= \frac{1}{2 \pi^2 n^2} \left(1-\gamma-\log (2 \pi n z) \right)$$
Which gives us:
$$J(z)=J_1(z)+J_2(z)+J_3(z)$$
$$J(z)=\frac{1}{2 \pi^2} \sum_{n=1}^\infty \frac{1}{n^2} \left(\gamma+\log(2 \pi) + \log z+ \log n \right)+ \\ + \frac{1}{2 \pi^2} \sum_{n=1}^\infty \frac{1}{n^2} \left([2 \pi n z \cos (2 \pi n z)-\sin (2 \pi n z) ] \left(\operatorname{Si}(2 \pi n z)-\frac{\pi}{2} \right) - \\ -[2 \pi n z \sin (2 \pi n z)+\cos (2 \pi n z) ] \operatorname{Ci}(2 \pi n z) \right)$$
The first part is simple:
$$J_1(z)=\frac{\gamma+\log(2 \pi) + \log z}{12}$$
$$J_2(z)=\frac{1}{2 \pi^2} \sum_{n=1}^\infty \frac{\log n}{n^2}=- \frac{1}{12} (\gamma+ \log(2 \pi))+\log A$$
So:
$$J_1(z)+J_2(z)=\frac{\log z}{12}+\log A$$
The rest of the series have a very complicated form, unless $z$ is an integer or half-integer.
$$J_3(z)=\frac{1}{2 \pi^2} \sum_{n=1}^\infty \frac{1}{n^2} \left([2 \pi n z \cos (2 \pi n z)-\sin (2 \pi n z) ] \left(\operatorname{Si}(2 \pi n z)-\frac{\pi}{2} \right) - \\ -[2 \pi n z \sin (2 \pi n z)+\cos (2 \pi n z) ] \operatorname{Ci}(2 \pi n z) \right)$$
Note though the identities from Wikipedia:
$$\int _{0}^{\infty }{\frac {\sin(t)}{t+x}}dt=\int _{0}^{\infty }{\frac {e^{-xt}}{t^{2}+1}}dt=\operatorname {Ci} (x)\sin(x)+\left[{\frac {\pi }{2}}-\operatorname {Si} (x)\right]\cos(x)$$
$$\int _{0}^{\infty }{\frac {\cos(t)}{t+x}}dt=\int _{0}^{\infty }{\frac {te^{-xt}}{t^{2}+1}}dt=-\operatorname {Ci} (x)\cos(x)+\left[{\frac {\pi }{2}}-\operatorname {Si} (x)\right]\sin(x)$$
With some care we can find an alternative form for the series which will very likely lead to Clausen functions, at least for some special values of $z$.
$$J_3(z)=J_4(z)+J_5(z)$$
Note that we can represent the integrals as:
$$\int _{0}^{\infty }{\frac {\cos(\pi u)}{u+ 2 n z}}du= \sum_{m=0}^\infty \int_{m}^{m+1} \frac {\cos(\pi u)}{u+ 2n z} du=\sum_{m=0}^\infty (-1)^m \int_0^1 \frac {\cos(\pi u)}{u+m+ 2n z} du$$
$$\int _{0}^{\infty }{\frac {\sin(\pi u)}{u+ 2 n z}}du= \sum_{m=0}^\infty \int_{m}^{m+1} \frac {\sin(\pi u)}{u+ 2n z} du=\sum_{m=0}^\infty (-1)^m \int_0^1 \frac {\sin(\pi u)}{u+m+ 2n z} du$$
I think the solution lies on this path.
It's especially clear why $z=1/2$ gives the most simple form.
Repeated integration by parts gives us:
$$\int_0^1 \frac {\sin(\pi u)}{u+m+ 2n z} du = \frac{1}{\pi} \left(\frac{1}{m+ 2n z+1}+\frac{1}{m+ 2n z} \right)-\frac{2}{\pi^2} \int_0^1 \frac {\sin(\pi u)}{(u+m+ 2n z)^3} du$$
$$\int_0^1 \frac {\cos(\pi u)}{u+m+ 2n z} du = \frac{1}{\pi} \int_0^1 \frac {\sin(\pi u)}{(u+m+ 2n z)^2} du$$
Which separates the expression into four double series:
$$S_1(z)=-\frac{z}{\pi^2} \sum_{n=1}^\infty \sum_{m=0}^\infty \frac{(-1)^m}{n(m+2nz+1)}$$
$$S_2(z)=-\frac{z}{\pi^2} \sum_{n=1}^\infty \sum_{m=0}^\infty \frac{(-1)^m}{n(m+2nz)}$$
$$S_3(z)=\frac{2z}{\pi^3} \sum_{n=1}^\infty \sum_{m=0}^\infty \frac{(-1)^m}{n} \int_0^1 \frac {\sin(\pi u)}{(u+m+ 2n z)^3} du$$
$$S_4(z)=\frac{1}{2\pi^3} \sum_{n=1}^\infty \sum_{m=0}^\infty \frac{(-1)^m}{n^2} \int_0^1 \frac {\sin(\pi u)}{(u+m+ 2n z)^2} du$$
Note that the last two series have the same order of convergence.
Summation w.r.t. $m$ of the first two series gives us:
$$S_1+S_2=-\frac{z}{2\pi^2} \sum_{n=1}^\infty \frac{1}{n} \left(\psi(zn+1)-\psi(zn) \right)=- \frac{1}{12}$$
So then:
$$J(z)=\frac{\log z-1}{12}+\log A+S_3(z)+S_4(z)$$
If we collapse the $m$ series again in $S_3,S_4$ the new integrals and the $n$ series will converge absolutely, unlike the original ones. So, there may be some nice way to evaluate them.
$$S_3(z)=\frac{2z}{\pi^3} \sum_{n=1}^\infty \frac{1}{n^3} \int_0^\infty \frac {\sin(\pi n u)}{(u+2 z)^3} du=\frac{1}{2\pi^3 z} \int_0^\infty \frac {\operatorname{Sl}_3(2\pi z u)}{(u+1)^3} du$$
$$S_4(z)=\frac{1}{2\pi^3} \sum_{n=1}^\infty \frac{1}{n^3} \int_0^\infty \frac {\sin(\pi n u)}{(u+ 2 z)^2} du=\frac{1}{4\pi^3 z} \int_0^\infty \frac {\operatorname{Sl}_3(2\pi z u)}{(u+1)^2} du$$
The second kind of Clausen functions $\operatorname{Sl}_n$ are sometimes denoted as $\operatorname{Gl}_n$.
Let's take:
$$z= \frac{1}{q}, u = q v$$
$$S_3 \left(\frac1q \right)=\frac{q^2}{2\pi^3} \int_0^\infty \frac {\operatorname{Sl}_3(2\pi v)}{(qv+1)^3} dv=\frac{1}{2 q\pi^3} \sum_{m=0}^\infty \int_0^1 \frac {\operatorname{Sl}_3(2\pi v)}{(v+m+1/q)^3} dv$$
$$S_3 \left(\frac1q \right)=-\frac{1}{4 q\pi^3} \int_0^1 \operatorname{Sl}_3(2\pi v)~ \psi ^{(2)}\left(v+\frac{1}{q}\right) dv$$
$$S_4 \left(\frac1q \right)=\frac{1}{4 \pi^3} \int_0^1 \operatorname{Sl}_3(2\pi v)~ \psi ^{(1)}\left(v+\frac{1}{q}\right) dv$$
For $0<v<1$ it turns out that $\operatorname{Sl}_2(2\pi v)$ are represented through Bernoulli polynomials, so:
$$\operatorname{Sl}_3(2\pi v)= \frac23 \pi^3 B_3 (v)= \frac26 \pi^3\left(v-3v^2+2 v^3 \right)$$
So we get:
$$S_3 \left(\frac1q \right)=-\frac{1}{12 q} \int_0^1 (v-3v^2+2 v^3 )~ \psi ^{(2)}\left(v+\frac{1}{q}\right) dv$$
$$S_4 \left(\frac1q \right)=\frac{1}{12} \int_0^1 (v-3v^2+2 v^3 )~ \psi ^{(1)}\left(v+\frac{1}{q}\right) dv$$
Using integration by parts:
$$S_3 \left(\frac1q \right)=\frac{1}{12 q} \int_0^1 (1-6v+6 v^2 )~ \psi ^{(1)}\left(v+\frac{1}{q}\right) dv$$
$$S_3 \left(\frac1q \right)+S_4 \left(\frac1q \right)=\frac{1}{12 q} \int_0^1 (1+(q-6)v+3(2-q) v^2 +2q v^3)~ \psi ^{(1)}\left(v+\frac{1}{q}\right) dv$$
Using integration by parts again:
$$S_3 \left(\frac1q \right)+S_4 \left(\frac1q \right)=\frac{1}{12 q} \left(\psi \left(1+\frac{1}{q}\right)-\psi \left(\frac{1}{q}\right)\right) - \\ - \frac{1}{2 q} \int_0^1 \left(\frac{q}{6}-1+(2-q) v +q v^2\right)~ \psi \left(v+\frac{1}{q}\right) dv$$
So we have:
$$J (z)=\log A+\frac{z}{12} \left(\psi (1+z)-\psi (z)\right)+\frac{\log z-1}{12} - \\ -\frac{1}{2} \int_0^1 \left(\frac{1}{6}-z+(2z-1) v + v^2\right)~ \psi \left(v+z\right) dv $$
Using integration by parts again:
$$J (z)=\log A+\frac{z}{12} \left(\psi (1+z)-\psi (z)\right)+\frac{\log z-1}{12} - \\ -\frac{1}{2} \left(\frac{1}{6}+z\right)~ \log \Gamma(1+z)+\frac{1}{2} \left(\frac{1}{6}-z\right)~ \log \Gamma(z) + \\ + \frac{1}{2} \int_0^1 \left(2z-1 + 2v\right)~ \log \Gamma \left(v+z\right) dv $$
We got back to the log-Gamma integral, but a litle bit different. Changing $v=t-z$, we get:
Using this and comparing to the original integral, we get a curious identity:
$$\int_0^z \log \Gamma(t) dt- \int_z^{1+z} \left(t-\frac{1}{2} \right) \log \Gamma(t) dt= \\ = \frac{z}{12} \left(\psi (1+z)-\psi (z)\right)- \frac{z(1+z)}{2} \log z+ \frac{z(z+2)}{4}+\log A- \frac{1}{12}$$
Or, if we denote:
Seems not very useful in this case, however it could be a nice definition for the Glaisher-Kinkelin constant.