I have a Primary Arms 3x Deluxe on a Larue flip to side mount (I think the LT755). I had to take my rear BUIS off because the magnifier wouldn't close with it on. I measured it a while back, and I think the Magpul MBUS will clear it by something like .15".
EDIT: I just re-measured. Clearance with Larue LT755-S mount and Primary Arms 3x magnifier is roughly .62". Magpul's website states the MBUS Gen2 measures .51" above rail, so it would be cutting it close. With the Primary Arms magnifier, you are pretty limited on BUIS options. Not sure how others are, might be the same for most. I'm still more than happy with my Primary Arms magnifier, would definitely recommend it. I'm thinking it was only around $70, definitely affordable and quality.