The possibilities for inadvertently creating a lack of balance increase with different factions, that’s true. At the same time, Wingspan, which I guess FrankJones alluded to, shows that you don’t need factions for creating a lack of balance so severe that house rules had to turn into near-standard rules, not only for competitive players but also for many regular players. There are not many games that had factions banned. Normally, regular players are fine with the factions and competitive players want to bid on factions anyway. I think Gaia Project is a good example for that. There are factions that are strong, there are generally weaker ones and some highly situational ones, but none is considered clearly OP afaik, not even Taklons or Ivits. I think having to live with that is ok, given the massive variety that comes with the factions in GP.
Personally, I don’t like games with extreme asymmetry like Root or Ahoy, but that’s just me, I see many people enjoy these a lot. I think it’s a good thing that while asymmetry is clearly on the rise, both in the GP way and in the Root way, there are still new and complex games that only have slight asymmetry. I wouldn’t like it if asymmetrical factions would become a new standard. Variety is great, not only in a game, but also in regard to the board games market in general.
Edit: Some of that OP talk can also be misleading. I've recently started playing Watergate, an asymmetric 2p-game. On BGG, you'll find nearly as many posts saying playing the editor is OP as posts that say playing Nixon is OP.