Make objects invisible as they pass behind non rendering geometry

I have a rather interesting challenge today.

I have a cylinder that animates along a track and passes through several small tubes rotating tubes. However, I need to render each of these elements out individually (with an alpha background) and then recombine them in a program that lacks any real masking capability.

So the problem I've found is that when I recombine all the layers, since I can't use masks, the cylinder will either be on in front of or behind the loops rather than passing through them.

I know 3DS max has an alpha matte material that can be used to solve this problem, and I'm wondering if C4D has something similar so that I can render out these loops in their own pass, but they will still become transparent when the non rendering cylinder passes in front.

Sorry my question is a little convoluted, it's an easy thing to visualize but difficult to vocalize.