POTUS would have the 747s or 757s available. I don't know who makes the decisions which. But Trump often used the 757 on shorter flights, I assume in part, to keep costs down. Just look at almost any rally at an airport for evidence. The 747s would also be a bit more limited to which airports could service them. I assume all AF bases would be able to handle a 747 but not all AF bases are near where POTUS needs to be. Anyway, I think it's only mildly of interest that he didn't fly on one of the 747s, in so far as, perhaps the military not wanting to give him that kind of honor.
Yer right though, most important thing is not which plane but which call sign was used.