I think the problem with using an optical perf sensor is how you handle different gauges. if the scanner has to do 16 and 35, the perfs are in totally different positions. Our old Imagica 3000V had perf sensors and they worked great. They were Keyence red laser proximity sensors, but that scanner was only 35mm, so it was easy to set up in a fixed position and tune them to look for the perfs.
The other issue with using sensors is what happens when you hit a section of broken or missing perfs? A better method is an encoder wheel that measures how far the film has moved across a capstan or PTR roller. That gives you an approximate idea of where you are (not accounting for shrinkage). Then the image can be taken and aligned in software. Shrinkage can be calculated to adjust the distance the film moves between exposures based on what you learn from the registration algorithm with each frame. Since shrinkage can vary in a reel, this needs to be an ongoing process. But at least if you have broken perfs, you have a backup positioning system from the encoder.
As long as the gate is big enough to allow for some slop, this should work fine.