A level tone hole makes it much easier to seat a pad, but very few saxophones (none that I've seen) have truly level tone holes when they leave the factory. This is, I believe, due to the nature of the manufacturing process and the fact that metal has memory.
When tone holes are created on most modern saxophones, they are extruded, or "drawn" (stretched) from the brass of the body, and then cut to "level" at the factory. Some saxes have extruded tone holes with a rolled edge (Conn) and a couple have soldered-on tone holes (King, Martin). For the purposes of this article, I'll be talking only about the extruded tone holes found on Conns, Selmers, Yamahas, Yanigisawas, and other "drawn" tone hole saxophones (most saxes).