Roglic gifted him a stage win, this was clear at the time. Jumbo Visma later basically confirmed this in their documentary. I think circumstances were definitely favoring Pogacar, even when he was dropped, they never actively started pushing to distance him, simply because they didn't see him as a rival (i can only assume). However, i do think he earned his podium spot, Quintana and Lopez really underachieved imho and Pogacar proved he was stronger in more instances than the other way around.
The thing is, as strong as he was in the Vuelta, for his age and experience, i'm not sure how far he could go in this TDF. I'm still convinced the field of competitors in the Vuelta was really weak, and i fear his Vuelta podium might not relate as favorably to a ranking in the TDF as many assume.