Headmaster acid declares to the prejudice teachers that they can't pass Squall but not Seifer as they both willfully disobeyed orders. Nida gets sent to Timber with Zell as lead.
Right before or after the SeeD request comes in the specifically calls for the skills of a gunblader. Maybe an older SeeD who SxS respect brings it in and offers an alternate exam. Something like a monster invasion of dragons and they need the gunblade's ability to cut through anything solid to win. SxS work well together because rivals=equals and they respect each other if no one else. I think Seifer would follow the orders of someone he respected and trusted, like an older combat pragmatist, aka you'll follow my orders or you'll die.
This follows the theory that more time is passes in between those first few events than we think, a couple of days between the exam and the ball, a couple more between the ball and the mission to Timber a couple of days in Timber a couple of days getting to G-garden a couple of days in Deling City waiting for the parade so on and so forth. Giving time for word to get to Squall and Seifer that something's happening to their home. So they catch up to Garden at FH only they've literally been doing nothing but stopping an invasion from the Island closet to Hell for the last month and are level 100ish. Much like he would have in Dollet they announce their presence right before the heavy machinery attacks their friends, hey galbabian soldiers don't leave me hanging now. They slice open the side of the mecha freeing Selphie and co right before it explodes. They walk up to the previously cowed Cid and salute, "SeeDs Almasy and Leonhart reporting for duty."
Cid breathes a sigh of relief at the sight of the steely eyed young men and turns to the commanding officer who had been knocking the mayor and him about, "Behold General! Two of my best! A two man army if you will. I'd get out of town and call for a full retreat if I were you. Neither are known for their mercy." Playing the part SxS flank the Headmaster and lift their gunblades to point tauntingly towards the General who has just seen these young men jump from a bridge and carve open a tank with one blow. The General calls for a full retreat.
Cid indicates that the other orphans will catch SxS up on what's happening while he placates the FH mayor explaining that he was only bluffing and SxS were not homicidal maniacs. Nida who had taken Squall's place on the team has been trying to show himself as a leader but he's just so forgettable it's difficult. Instead Zell has emerged as a leader and steps forward to explain what's going on.