Even ultra-luxury manufactures like ALS don’t do this, and they do pretty much everything that’s conceivable. It actually is possible to complete via machining but watchmakers generally do not (iirc there are a few examples but none come to mind immediately).

At this point I honestly think it’s partly tradition. The movement is expected to be perfect and that’s where a lot of the labor cost goes in high end watches. Adding $30k to an APRO to have a guy scrape tiny flakes of the screw off over a few days would be a bit silly. I can see why it bothers you though, which is why AP went with the hexagonal center-aligned bolts. The problem is that you can’t really do that on every side of the case or you’d never get it apart again (or together in the first place) as the bolt needs a nut on the inside.

The front ones on the APRO aren’t actually screws, they’re bolts made to look like screws. Correcting the alignment would require the threads to be perfectly aligned and oriented in every direction with extremely close tolerances.

Further reading:

https://www.hodinkee.com/articles/why-screw-slots-arent-aligned-in-watchmaking

https://www.esquire.com/uk/watches/a33816691/why-dont-screws-line-up-watch/