At the moment, this mod affects a single scene on Peragus and a single scene on Onderon with potentially more scenes/content to be restored in the future. Considering PS, EE, GL and M4-78 don't touch Peragus that'll be clean, EE, GL and M4-78 don't touch Onderon so that'll be clean and considering niether Disciple or Handmaiden have a role in the Bounty Hunter ambush I'm willing to bet that'll be compatible as well.
In short, everything is safe to use with the Mod Collection.