Good repair C_Kelly!
Yes you’re correct. It was deliberate. This is a quick yet unacceptable fix that you see much too often. You’ll see marks like you mention that look like they were pushed up with a graver and others that are just punch marks. Many times when changing a balance staff the replacement may be a tiny bit longer than necessary. By raising the metal under the balance cock one can compensate for the extra length. Also balance cocks sometimes get bent down for whatever reason and this method is used to raise or tilt the balance. You’ll also run across small shims (paper, brass sheet, aluminum foil etc.) placed under the balance cock foot.
The correct repair for an over length staff is to grind and polish a little off one or both pivots for a proper fit. It actually only takes a minute to do the job properly. I keep a Levin Pivot Polisher base mounted to the edge my bench which the tool mounts onto when needed. This is an excellent tool to have handy. For jobs that need a bit more attention a jewelers lathe and a small assortment of balloon chucks will do most jobs quickly.
It’s late tonight so I’ll take a couple of pictures of the Levin Polisher in the morning and will post them up here.