I did toy with the idea that you could just use several beam splitters to get your three images,
If you are talking about partially-silvered mirrors, I'm not sure if it would work as well as you hope. Usually optical mirrors are silvered on the front surface, so that the light isn't refracted twice from traveling through the glass on the front of a conventional mirror. If you used a partially silvered mirror, the light that bounced off the front would go one way, and that that went through the mirror would go another way.

This might be fine depending on what your criteria are for alignment. It seems to me that if I were doing it, I would just give up on trying to get the 3 negatives exposed so the images were perfectly aligned when you stacked them up for printing. You would need a lot of precision to do that. But if you can resign yourself to visually lining up the negatives on a light box, then your camera just has to have the same magnification between the 3 negatives, and they can be misaligned by quite a bit (whole mm) without it being a problem.