I would be surprised if the team (or rather their sponsors) easily okays skipping the Tour. But I’m not sure how different that aspect (brand promotion) is when it’s a country sponsoring a team rather than a company?
Given Pogacar status in the team I think he has something to say and they won't oppose if he wants to skip the Tour one year (especially after completing the double and regaining the Tour title). It's still a long way to go and a lot of things can happen in the meantime. Tour is always his big goal but I can imagine him intentionally skipping it once during his prime (i.e. to have a better shot at Roubaix and Vuelta).