The way I always figured crafter/gatherer dungeons would work is:
Full party with the typical 1 tank, 2 DPS, one healer setup, then 2 gatherers, 2 crafters.
Think along the lines of a Tower Defense game.
The main battle party works to cull and slow down the monsters coming through with every wave, increasing in difficulty as the next wave comes.
The gatherers all have nodes and gathering points to gather items called "Resources", literally just "resources". Generic all-purpose name for an all-purpose material.
The crafters use these Resources to craft and use various items around the dungeon which help the battle and support the battle party while they beat down the monsters.
The better the gatherer, the more HQ resources you get, which makes it easier to HQ the things around the dungeon to make them stronger.
Or, if your crafters are good enough, they can just focus on getting as many as resources as possible.
This helps keeps the monsters down and the more waves you make it through gives you a better reward, with a chest for the crafters, a chest for the gatherers, and a chest for the battle party, giving them all a reason to play on the type of class they need stuff on. I dunno really what the reward would be, maybe like materia or demimateria something, but I'm sure SE could figure that out.