I think this should be easy.
The same way you can bypass and manipulate audio inserts, send, EQ,etc, through a Generic Remote, why not also make it possible to assign control for Midi Inserts and Modifiers? At least the Bypass option and Record Output to Track.
This makes it very handy to change between keyboard velocity, or some preset done in the Midi Inserts that can be useful. I understand most of that stuff can be done on the PLE (and assign key command), but this looks like a a feature that should be included, just like the already existing ones.