Well everything has been tested extensively by Risewild, including firing all followers in both wastelands. Any mods that alter vanilla companions are going to need to be updated to have a patch for this when it's integrated. The Fallout 3 companion stuff will be in TTW itself, while the NV stuff will be an optional plugin.
We're not interested if it works or not with other mods, that's on those mods to address. TTW stuff is built to be used stand alone (think vanilla). The only bugs that were "fixed" were ones that were either making it difficult to get everything working inside the framework, or because they were just dumb and easy to fix. The latter ones may end up getting removed since they don't affect how the dialogues/wheel work. They've been included as of now because I felt like doing them, and they were easy things to fix, and have little chance of interfering with other mods.