Player Caused?
I have leveled sax tone holes and years later looked at them again. Still level after all these years, on horns that were "rode hard and put away wet".
If player bumps a key guard against something, you can bet the respective hole got changed. But otherwise, ordinary playing does not seem to change the chimneys.
Selmer draws and levels their tone holes in one process on the raw body tube. You can see that in their video. That is the only time those holes are level. Then they use torches and start adding ribs and posts, and they mount hardware and connect bow joints and everything else. How can a flimsy body tube survive all that heating and building? If the builder waited until he got the ribs, posts, et. al. on and then leveled the holes, things would be better.
I once made the mistake of leveling a low Eb hole with the bow ring disconnected on a Selmer SA80II alto. When I replaced the bow ring, it squeezed the body tube just enough to cause that hole to become unlevel again.
During overhaul, techs know to make sure the key guards fit easily into their mounting brackets, because forcing on a mis-aligned key guard can bend the tone hole.
Clarinets and saxophone pad/tone holes are different beasts. Clarinet pads are softer, tolerate greater departures, and are small diameter. When we are dealing with tone holes requiring a 52 mm pad, operated by a compound lever a foot long with all sorts of torque issues, techs are indeed concerned about level rims.