Unknownreported this bug
We went ahead to make absolutely sure that it was purely just MDungeons and MV Inventories conflicting. Booted up the test server with MDungeons and without Inventories installed. It worked perfectly fine and inventories were consistent.
We then installed MV Inventories and started up again, and the issue immediately arose. So yeah, it seems like a clear conflict there. We fully rely on MV Inventories and can't use MDungeons as long as that conflict exists sadly.
And yes I've done everything MV allows to not affect the dungeon worlds and that did squat.