Wow, that's quite impressive!
It reminds me of the ancient project I made before the StereoPi - it was a mirror rig to get a stereoscopic image from a single camera (it's on the right of the photo). And this project is 10 years old. It motivated me to develop a StereoPi
I remember that aligning the mirrors was extremely difficult, but the software finally does most of this. In your case, the affine transform can be automated, so you exclude the manual adjustment.
By the way, when I read your post, my first idea was to use a camera with a physically removable IR filter (by servo motor, for example). But then I realized that the pictures would be taken at different times, and any moving object would ruin the result.
Eugene a.k.a. Realizator