Still all sounds like things that either already exist in Reaper or could be done via JS and thoughtful routing.
Every couple of days it seems somebody asks the forum how to change presets in a plugin via program change message. I guess I've never read one of those threads because I don't need it, but I'm sure it's been pretty well figured out by now. Even if it can't be done, it's still not a lot more than bypass and/or mute automation.
Realtime controller re-mapping is easy. Pretty sure there's a JS plug or three that come with Reaper to do it.
Remember that each "track" in Reaper has a whole lot of parallel audio and MIDI channels to work with, and routing between them is pretty easy. Then there's the things you can do with parameter modulation and linking... I just really don't think you're making this out to be harder than it is. I think it's important to understand the various aspects you've brought up in this thread, but I don't think you need to re-write reaper to do what you want to do.
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