The fact that you need two warm bodies actually coordinating and cooperating to make the gat/flak combo "OP" means it's not OP.
While you do have a point that it does encourage teamwork, the main problem is that there is no other weapon combination in the game that can do the same thing (which also has the knock-on effect that the only ammo type worth a damn is heavy clip, every other ammo type is redundant, making gunners useless). There are only 2 other armour-stripping weapons in the game (mercury field cannons and harpoons), and absolutely nothing that can strip armour in the heavy weapons category. This would even the playing field for captains selecting loadouts, and be a lot less restrictive. With the reload times on a lot of the guns (allowing enemy engineers enough time to bring the hull back up) it would still need teamwork to have one player with piercing and one with explosive in order to guarantee the kill.