In answer to my own question, the equality can be shown as follows. First, we realize that $\int_0^{2\pi}\int_0^b\int_0^b r_1r_2\frac{J_1\left (\alpha\sqrt{r_1^2+r_2^2-2r_1r_2\cos(\theta)}\right )}{\alpha\sqrt{r_1^2+r_2^2-2r_1r_2\cos(\theta)}} dr_1dr_2d\theta\\=\frac{1}{2\pi}\int_0^{2\pi}\int_0^{2\pi}\int_0^b\int_0^b r_1r_2\frac{J_1\left (\alpha\sqrt{r_1^2+r_2^2-2r_1r_2\cos(\theta_1-\theta_2)}\right )}{\alpha\sqrt{r_1^2+r_2^2-2r_1r_2\cos(\theta_1-\theta_2)}} dr_1dr_2d\theta_1d\theta_2$
From here we notice that $\sqrt{r_1^2+r_2^2-2r_1r_2\cos(\theta_1-\theta_2)}$ is the distance between two particular points in the circle of radius $b$. Let that distance be denoted as $L$.
Then we have
$\frac{1}{2\pi}\iint_{A_1}\iint_{A_2}\frac{J_1(\alpha L)}{\alpha L} dA_1 dA_2$.
We can write this instead as
$\frac{(\pi b^2)^2}{2\pi}\int_0^{2b}\frac{J_1(\alpha L)}{\alpha L}p(L) dL$, where $p(L)$ is the probability density of choosing two points of distance $L$ within a circle of radius $b$. This probability density is well known. See for instance equation (5) of Ricardo GarcĂa-Pelayo 2005 J. Phys. A: Math. Gen. 38 3475 doi:10.1088/0305-4470/38/16/001 and references therein.
We have $p(L)=\frac{L}{\pi b^2}\left ( 4\cos^{-1}[d/(2b)]-L\sqrt{4b^2-L^2}/b^2 \right ), 0\leq L \leq 2b$
The integral can now be easily evaluated and gives the required equality.
This technique is usable any time the integrand is a function of only one parmater, like L in this case.