Yes... The M65 implementation is having to keep to the "spirit" of the C65 specification since it was incomplete.
However, the potential for the feature is there and it certainly makes sense to implement it and I don't think it would be terribly difficult to do.
I think to make using the DMAgic really useful to games and the like, implementing the INT bit feature is important. Otherwise, you're always going to be limited to terribly short DMAgic job runs and juggling them with your IRQ handler and raster timing is going to be a real pain.
If its not implemented now, its certainly something people are going to ask for. I know I would want it.
The idea is to actually finish the M65 implementation and "C65 compatibility" is really not something that should be particularly high on the "need to have" list. Like you said, there are quite significant differences between the revisions. Compatibility with them all is impossible. Existing C65 software (which there is very little of) can be easily patched and even has to be, just to run on a variety of C65s.
Personally, I'd rather see a feature-rich M65 implementation that is incompatible with certain C65 revisions or even all of them if needs be, than one that is dumbed-down in order to try to be compatible with something that was never realised and barely used.
The C65 as a working machine standard is a concept, not a reality at all. That's the truth. There is no such thing as "C65 compatible" and never will be.