Assuming every parameter is constant except for the variable $t$, how does the author get from

to here
?
When I integrate velocity myself I get $$z(t)=v_0t+\frac{v_e(m_0-qt)(\ln(1-\frac{qt}{m_0})-1)}{q} -\frac{gt^2}{2}$$ which leads to totally different results when using the same parametric and variable values. Specifically I can't understand how does he get rid of the $-1$ in the second parenthesis, and where does $(v_0+v_e)t$ come from.
There is an implicit assumption that you may have overlooked here.
In physics, the convention is that the initial position is zero, i.e. $z(0) = 0$. Therefore, you should first write your integral as,
$$z(t) = Z + v_0t+\frac{v_e(m_0-qt)}{q} \left[ \ln\left(1-\frac{qt}{m_0}\right)-1 \right]-\frac{gt^2}{2} \tag{1}$$
Then, find out $Z$ by setting $z(0)=0$, which yields,
$$Z = \frac{v_e m_0}{q}$$
Now, plug the value of $Z$ back into (1), you get
$$z(t) = (v_0+v_e)t+\frac{v_e(m_0-qt)}{q}\ln \left(1-\frac{qt}{m_0} \right) -\frac{gt^2}{2} $$
The resulting $z(t)$ is guaranteed to be zero at $t = 0 $.