1. Cultural Assistance: Now I don't know if this happens all the time or only with the TEC rapid development research, but using this ability on my fully teched TEC ally's home world caused the build time for the first tactical slots upgrade to jump from 35 seconds to 600 seconds (check it with the developer.exe), effectively making this ability a negative buff.
2. Cultural Integrity: This one isn't a negative buff, it just fails to do anything. Check my upload save below, you'll see that despite the buff being correctly applied with the "invulnerable" text on the infocard, it does nothing to stop two Desolators and their bombardment platforms from damaging my ally's homeworld. If you wait long enough they'll probably even destroy the planet with the invulnerability buff still on. Good news is this can be fixed without an engine change, just use the "PlanetBombingDamageAbsorption" entity modifier set to 1.0. For any modder wanting this it is fixed in my Enhanced 4X Mod.
3. Harmony: This one is pretty understandable, but if you look at the green enemy desolators soon after the save you'll notice they receive the same 5% hull, shield and antimatter regeneration buff as the ally my envoy is trying to help. This is because the buff uses the same AlliedOrEnemy target filter that all the envoy abilities use. Ideally it should only effect the units of the planet owner, as its pretty silly that my envoy would help a player I get no relationship bonus with, especially on locked teams.
I'm guessing these major bugs went uncaught because still no one really uses envoys and Advent doesn't get used much since 1.3, but still, they really should be patched ASAP.
Save: Advent envoy issue.save; Vanilla Diplomacy 1.34. Developer.exe was used to spawn all the ships needed to demonstrate and give all research.
And just a minor plea here, I realize IC and/or Stardock is probably tired of trying to give Sins genuinely good Diplomacy. I don't blame you, I'd much rather you focus on all the stuff in Rebellion people probably care more about anyways. However, at the least could you restore some of the Diplomacy functionality of the Gameplay.constants file that was removed in v1.3. I believe Modders like myself who can afford to tweak numbers far longer and more often than you can are more likely to find a balance that works, and allowing us to change more values in the playerDiplomacyAIDef section (especially the TreatyRelationshipChanges) would be a big help.