Why aren't these two integrals equal?
$$\int_0^\pi \int_{-1}^{1} e^r \,dr\,d\theta \qquad\neq\qquad\int_0^{2\pi} \int_{0}^{1} e^r \,dr\,d\theta$$
Let me explain why I'm asking.
This is the change of variables theorem for double integrals:
Now, suppose that we have the unit disc $D \subset R^2$ and the transformation $T$ given by $x=r\cos\theta$ and $y=r\sin\theta$. Then the rectangle in the $r\theta$-plane $-1 \leq r \leq 1, 0 \leq \theta < \pi$ maps injectively to the unit disc under $T.$
So in theory, it seems like we should be able to integrate in polar coordinates using this region $-1 \leq r \leq 1, 0 \leq \theta < \pi$, in addition to the "usual" region $0 \leq r \leq 1, 0 \leq \theta < 2\pi$.
Then why aren't the above two integrals equal, and more importantly, why does this not violate the change of variables theorem?

Let's start from the "usual" region version and work backwards to get an integral in terms of $x$ and $y.$ One simple way to do this with the polar transformation we're used to is to simply factor out an $r$ for our Jacobian:
$$\begin{aligned} \int_0^{2\pi} \int_0^1 e^r dr d\theta &= \iint_R \frac{e^r}{r} r dr d\theta \\ &= \iint_D \frac{e^{\sqrt{x^2 + y^2}}}{\sqrt{x^2 + y^2}} dy dx \end{aligned}$$
noting that we can say $r = \sqrt{x^2+y^2}$ here because $r$ is always positive in our region.
However, if we want to solve this same integral using the other parametrization of the unit disc then we have to note that because $r$ is negative over some parts of the region, we have to use $\sqrt{x^2 + y^2} = |r|$ so we end up with a slightly different integrand:
$$\begin{aligned} \iint_D \frac{e^{\sqrt{x^2 + y^2}}}{\sqrt{x^2 + y^2}} dy dx &= \iint_{R_2} \frac{e^{|r|}}{|r|} |r| dr d\theta\\ &= \int_0^{\pi} \int_{-1}^1 e^{|r|} dr d\theta \end{aligned}$$
noting that the absolute value around the determinant of the Jacobian also cannot be dropped in this case.
Now, noting that the integrand is even in $r$, we will see that the result of this integral will match the result of the first.
$$\begin{aligned} \int_0^{\pi} \int_{-1}^1 e^{|r|} dr d\theta &= \left(\int_0^\pi d\theta\right)\left(\int_{-1}^1 e^{|r|} dr\right)\\ &= \pi \left(2 \int_0^1 e^{|r| }dr\right)\\ & = \left(\int_0^{2\pi} d\theta\right)\left(\int_0^1 e^r dr\right)\\ & = \int_0^{2\pi}\int_0^1 e^r dr d\theta \end{aligned}$$
So ultimately, the reason that the two proposed integrals don't match is simply that they don't correspond to each other.