I see, so the indiMKII has sacrificed perfect reproduction for maximum output flexibility. I suppose that is understandable given the huge variety of displays that it's expected to work with but still,
You're idea of running the amiga off a clock from the indi is interesting. Sounds like how a genlock works. No idea if the indi has access to the required pins to pretend it's a genlock and I've also seen some smooth scrolling stuff do strange things when a genlock is attached. Probably a no goer.