I was casting gas check 316299's for my .303's and had some dud bullets on which I wasn't holding the sprue plate down at the hinge pin when I cut them off. The result was that those slugs had a bit of a stem on their bases.
Rather than melt them back down, I decided to make a science project out of them. Seated gas checks through my NOE push-through arrangement as normal, which more or less molded the gas check over the bump, leaving a visibly different base than the slugs that were cut off clean.
10 rounds of clean bases versus the 10 lumpy ones. Same powder charge, same distance, same day:
So yeah. . .square bases matter, and covering their butts with copper doesn't solve the problem.