So they can be legal.
That way, if you buy a WBO painted bey or send yours in for a WBO paint job, you can use it in WBO tourneys.
The level chips are to make them more easily accessible.
No.
Paint adds weight, can rub off on other bets, and generally mess aerodynamics up
This comes with a variety of issues such as quality control, legal methods of modification, what kinds of paints may be used, proving that the modification is tournament legal for any specific part, finding people capable of and trustworthy enough to do this, and so on. Even if it was possible to do, it would be a total nightmare to enforce in a tournament setting.
Custom level chips have the same issue of quality control, since 3D printed chips aren't exact copies of real chips and don't usually balance things out exactly or fit as they should. It would similarly be hectic to try and come up with rules and regulations to allow them.