I'm using that as well, for PC. But I run my load order through LOOT, and force SSE to comply with LOOT's version. I trust LOOT. I DO NOT trust beth's setup. Then again, I don't play SSE much - because I don't have SSKE for SSE - so.... WAY too many mods I need aren't available.
@Macole: "for the most part" isn't anything to do with how NMM manages stuff. It's to do with losing power (a common occurrence here in the winter) while NMM is open - which means I lose my profiles, and there's no way to get them back. This is something that most people will never have to deal with.... I live in a very out-of-the-way area, and winter - well I LOVE me my winter - but losing power with NMM open.... it's seriously problematic.
I've gone to copying the ModProfiles folder to a backup drive every morning. Nope, doesn't help when NMM chokes (because there's no way to retrieve those profiles since no one ever bothered to make that an imperative) - but at the very least, I can figure out what each girl had active the last time I logged on, so I don't get the dreaded "missing files" message....