It would be a good idea to scrape off some of the finish on the bottom side of the transformer bell and just the smallest amount on the top side around each hole.
Cerakote would be a neat coating, but you have to follow the instructions very carefully. Skipping or modifying steps may lead to the coating flaking off. When in doubt, you could just take your parts to a reputable shop and have them done.
Most printers are intended to print on flexible material that travels through the printer rollers. I have seen people prepare a piece of very thin aluminum and send it through an inkjet, but you might need 8-10 tries to really get that right. Once your piece of thin aluminum comes out, then you could laminate it to the stock top plate and trim out all the inside holes. For what you're looking for, you may be able to find a local airbrush artist who would do a custom paint job on your top plate for you.