Yeah, I was thinking that second setup. Though I do wonder if you would strictly need a separate two lines or not. The MS can operate a couple of different ways, either in an 11 bit generic broadcast mode or their 29 bit proprietary setup. I think you'd still have to have an "repackager" either way as the MS CAN output is pretty limited in what you can change. The main thing I wonder is whether or not you could have two different protocols broadcasting on the same line or not. I can set up filters on all of my other CAN chips that would ignore stuff that wasn't addressed to that specific unit, but I'm not sure how the MS CAN controller is configured for that. For instance, my Arduino asks my Pi for the time to display on my dash gauge and the MS doesn't care, though I'm still using the MS format message packets for the sake of argument. I could always try changing them to a totally different setup just to see what happens I guess.
Ultimately I have a pretty limited number of controllers on the bus and I have complete control over 2 of the 3 of them, so I do wonder if I could make it work with just the single bus.