I realized almost immediately after posting that the notes feature was almost certainly in MO, I had just never noticed. Just checked and of course it is.
I'm so far away from an expert it's not funny, but without a way to view file conflicts a lot of what I like to do with modding becomes much more difficult/impossible. MO2 currently works almost exactly as well as MO and is still in active development as far as I know... I can't see a reason I would use anything else to mod a Bethesda game - except for that OBSE apparently has issues with MO, which is why I'm testing Vortex with Oblivion.
* actually after playing around more, it does indeed notify you of file conflicts and allows you to view them, and then set rules for how to manage conflicts between the two mods. Still lacks the ability to selectively 'hide' certain files, so you can only set one mods priority over another's files en masse, but it is helpful.
It's in alpha right now so I expect a lot of change... Honestly at the moment though it feels to me very much like NMM, just with a better interface and some extra features.
There seems to be an issue with the way it tracks install order, at least on my system / for Oblivion? It is simply not accurately tracking the order I installed my mods.