It's been a while since I played the campaigns. From what I remember, the DA campaign works fine under TA. The Apocalypse scenario in the DL campaign had the problem of the Dread Lords not being set to the correct Race ID, which means that you have to wipe out all other races to win. I'm not sure, if that got fixed, but I think I saw it mentioned in one of the changelogs. If it isn't, it should be relatively easy to do by editing the scenario file.

From all the mods, APT is currently the most campaign-friendly. The tech tree is pretty much like in the vanilla game, just with all the bugs fixed, so it shouldn't make any additional problems.

All the other mods change the tech trees (some more so than others), so it is very likely, that there will be problems in the campaigns. I may try to make my mod, Autumn Twilight, compatible later on. For now, however, getting the AI to research properly is my main priority.