Well, here's what I've found on the file I had before making this thread (installed expansion then M4, going to try M4 then expansion later);
Vash's corpse is there and Visas' dialog about her death plays, but I still get her datapad added to my inventory and can talk to T3 to head to M478 after escaping Sion.
There's nothing else new in the Academy.
I can't get to the Valley Floor (couldn't trigger it in the Academy). I can warp to the Valley Floor but can't progress, Jolee is invisible and can't be talked to but I see his name if I put the cursor over where he should be.
M478 progresses as normal.
My little hypothesis for when I try installing the expansion over M4 is: Vash will be dead, I will get no datapad, the expansion will be perfectly normal and I will be able to access M478 via console warp, but not by galaxy map.
I'll post my results when I'm able to test this; I hope this goes well, these mods are both significant as, if successfully combined they build on both Korriban and the fate of Vash, as well as restore more of what TSL was meant to be, and add some as well.