I would just paint it first. Really what the paint is doing is making it easier to clean off dirty finger prints and black coil dust in the future.

I dont think you will lose the dimples but keep in mind those dimples are guidelines. You are going to want to check the position of everything - especially mechs - for the best alignment before screwing stuff down. If i don’t like the location of a dimple i create my own with an automatic centre punch.

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I have gotten a lot of Mileage out of mine. But just be careful on the top side if you decide a new dimple is in order. It can crack the clear if you don’t remove some before you dimple (depending on how close you are to a through hole). Don’t ask me how i learned this....

I think if you take CanadianPinball’s suggestion to paint it with the underside facing down you should get no paint dripping into inserts.