The only way to level it out would probably be wet sanding. But with that, you would have to be very careful not to sand through the clear and get into your playfield paint.
It's definitely not from the factory like that. Someone has clear coated it at some point. It's usually caused by applying it too thick.
For the amount of work involved, along with the possibility of doing more damage, I'm with CrazyLevi on this one. Might be better off leaving it alone.