I have been loading .45 with the small primer, since I don't like to toss brass if I don't have to. I load all the small primer brass first. If I get a large primer brass it just leaves the primer in the cup. Since I use a Dillon 550b I can easily get the case out before I add powder and toss it into the right brass box for when I load the large primer cases. I don't apply so much force normally to set off a primer and I make sure there isn't any debris on the priming pin to crush the cap to the anvil. I think is is safer to load a little slower to try to avoid problems.
There is one advantage to loading small primer .45 cases. I don't have to change over to large primers if I have been loading small primers on the caliber I was loading before. It does save a little time.