Pogacar may stop doing the Tour at some point and focus on other races (doing his own schedule). In this case coexistance of Pog and Seixas is possible and they will clash only in Lombardy and Liege.
Your theory about Pogacar pivoting to his own "Greatest Hits" schedule makes sense on paper, but I struggle to see that rational split actually happening in the real world. Here is why:
1- The TdF Gravity Well: Tadej Pogacar is the undisputed North Star of cycling right now. For a team like UAE, the Tour de France is the only race that truly moves the needle for sponsors on a global scale.
2- The Power Shift: The moment another rider (Seixas) brings the Yellow Jersey home, the internal hierarchy of the team shifts. The winner of the Tour inherently becomes the most valuable asset.
3- Support Follows Success: If Pogacar steps away from the Tour to let Seixas lead, he risks losing his "Alpha" status. In pro cycling, the best domestiques, the biggest budgets, and the total tactical commitment follow the man who wins the Tour.
Even if they only "clash" at Lombardia or Liège, the power struggle happens in the service course and the boardroom months before. Pogacar knows that to keep the team entirely in his corner, he has to remain the king of the biggest race. I don’t think he’s ready to hand over those keys and the support that comes with them just yet.