I actually like that boost...
I use a m9 in the loop just for delays, verbs and modulations. All my gain stuff is analog (pedals and amp channels).
The boost is a lot more noticeable with over-driven sounds than with clean sounds. This is strange because being in the loop should mean that any gain on the preamp should be treated equally by the m9.
Anyway, I don't like to use modulation with over-driven tones. I just does not sound good to my ears. Unless I'm going for a drastic efect for just a bar or two for just that song... In that case the boost does a very good job making sure it will be heard!
On clean tones I actually think the volume compensation is almost spot on. I have no complains!
That said, I do have a real MXR Script phase 90 on the board, before the pre-amp, for the van halen type moments