i don't actively participate in the competition nor organizational sides of this tournament, so this should be taken only as additional info.
As this tournament takes shape, it's looking more like a berger system league (single round robin variant).
Further, if we look up with to a similiar competition, tackling the same potential issue of affiliate teams competing in the same league, we can see how european footbal- spanish La Liga handled the situation with FC Barcelona primary squad, and Barcelona B. According to their rules, affiliate clubs can never play in the same league. So even though Barcelona B gained promotion to La Liga (first spanish division), it needs to remain in the Segunda (the second division), and the next team with the most points after Barselona B wins promotion instead of them (in case they are not an affiliate of a club already in the first division).
Next up, if Barcelona A ever gets demoted to second division, even if Barcelona B finishes first, it must go in 1 division lower than their A club. Saying that, if club A stays in division 1, club B can still get relegated to division B unrelated.
All that being said, Barcelona B is de facto a reserve team to Barcelona A, and they can exchange players between themselves every gameweek freely as a compensation for the kind of relation with strict promotion/demotion rules.
All of this might be considered as too stiff or not fair to the team that won primotion, but i just tought i lay it out here.