From a pure design stand point, the VS Seeker shouldn't have issues with multi-floor caves/dungeons. Each floor is its own separate map internally, and the game only rolls the dice on trainers on-screen anyway, I believe.
I think Pikachu315111 is probably closer with not wanting to make additional teams, but specifically in the context of FRLG specifically this is pretty relevant for the SS Anne, Rocket Hideout, the top of Pokemon Tower & Silph Co; all of these feature trainers that are only there until you complete the dungeon. Similarly all the gyms are in-doors and those are one & dones even if the trainers remain. Rather than tjust set them to reuse the same team or only disallow it in certain dungeons it probably made sense to just not allow it in any dungeon. Also would be prety weird for the Channelers in Pokemon Tower, I suppose.
Other gameplay consideration, I guess, is that you're more likely to go to a route for trainers than a dungeon due to ease of access.
I think Pikachu315111 is probably closer with not wanting to make additional teams, but specifically in the context of FRLG specifically this is pretty relevant for the SS Anne, Rocket Hideout, the top of Pokemon Tower & Silph Co; all of these feature trainers that are only there until you complete the dungeon. Similarly all the gyms are in-doors and those are one & dones even if the trainers remain. Rather than tjust set them to reuse the same team or only disallow it in certain dungeons it probably made sense to just not allow it in any dungeon. Also would be prety weird for the Channelers in Pokemon Tower, I suppose.
Other gameplay consideration, I guess, is that you're more likely to go to a route for trainers than a dungeon due to ease of access.