The "one job per player" thing is not a big enough deal to matter outside really anything except savage and ultimates. Not even EX trials is this something that should matter. The content is designed to be clearable even if jobs overlap. You get a penalty to limit break build up if you have repeated jobs, but any mechanics in casual content that require the limit break, the game gives it to you.
Stagger your buffs. It takes just a couple lines of chat to ask the other person if they or you should put your big buffs on the 60 second burst instead of the 120.
Play them in a different order. Problem solved.