Sometimes it's small, like whether or not `\author{my name}` needs to be included in the preamble or in the main body. These are short but annoying. Sometimes it's very annoying. I'm glad that I've never tried to publish in a two-column journal (which might exist in math? I don't know) which would require more substantial superficial edits.
I always assumed that this was a deliberate source of friction, slightly raising the bar of entry so as to discourage a certain sort of submission. I don't say I agree with this, but that's what I thought.
This sounds like the sort of problem that latex would be great at solving: changing the look of an article just by using different document classes. And sometimes it is great --- but some templates are terrible, terrible, terrible. (And sometimes these terrible templates are for great journals! I see little to no correlation there).