The achievement displays "Research every subject in the Harmony Tree while researching no subjects in the Hostility, Security or Understanding Trees." (it says nothing about the Fleet Logistics, so I went doing only that) so I went just researching Harmony and Fleet size but I didn't get the achievement once I finished researching the last point in Harmony.
Playing with Research Victory enabled and researching only Harmony and Fleet Logistics (and winning by research) didn't give the "Advent Harmony Researcher" achievement, it does however finish the game with a "Research Victory" popup effectively finishing the game.
However, losing by a Research Defeat, like the AI beat you in completing the special last research to reach a Research Victory, you only get a message that X faction has won but doesn't end the game, you aren't given the option to "quit or continue playing" like when you win, it just is a small message without ending the game at all.
Save file (without Research Victory enabled): Advent Rebel, Harmony Achievement
Save File (with Research Victory enabled and at 95% special research complete for Victory): Advent Rebel Research Victory
Save File (with Research Victory enabled and 98% for Defeat): Advent Rebel Research Defeat