I too have loaded .45 ACP and .45 Auto Rim and seating Large Rifle primers flush can be a problem with some lots of casings. And loaded black powder rifle loads with pistol primers. The excuse in both cases was I was out of the right style and used what I had available. Duh.
My decision is it is best to use small pistol primer in pistol casings, small rifle primer in rifle casings, large pistol primer in pistol casings, and large rifle primer in rifle casings. If I don't have the proper type on hand, it is time to stock up on the right size, and not make do with what almost fits.
And don't develop a load with standard primers and then use magnum primers because that's all I have left.