I wasn't around back then, but if I recall how it used to work it was you always fought under what Grand Company you picked. However, Limsa / Maelstrom was the most popular by far so everyone always picked it, making things fairly unbalanced and also resulting in extremely long cue times as a result. So eventually they implemented an opt-in mercenary system of sorts to try and get some people to play for the other teams, and then changed it again by just removing the Frontlines GC restriction stuff and assigned everyone to one of the three teams randomly to make it always fill.

Some of the achievements though still track based on what GC your character is currently in. So if you're currently in the Immortal Flames GC, you can ONLY get progress for the Immortal Flames side of achievements when you do Frontlines, even if you get put on Adders / Mael team.,