I personally run all of my factors through the effects loop…Modfactor obviously included.
I have no complaints *whatsoever* and this is totally picking nits, but I do think that Modfactor would be the one factor that would benefit by having two sets of inputs/outputs that were assignable to each program. I realize that from a design and price standpoint this probably wouldn't be feasible, which is why it isn't there. But, it would have been a neat little bell and/or whistle.
Perhaps if the good people at Eventide decide, at some point, to come out with a "multi-factor" (as some here on the forum have requested) assignable inputs/outputs could be a consideration though…Just a thought.
Regardless… Eventide products, IMHO, stand head and shoulders above anything else that's on the market today and sound amazing *wherever* you decide to put them in your signal path.