+1 for the rain cap. That's what I've done on all my vehicles. It's the ONLY time I'll buy a Tram/Browning product. You can get them for a few bucks on Amazon. They're 'good enough'.
My dad removed the entire NMO mount on one vehicle once. He used the 3/4" snap in plastic/rubber plugs. He painted it to match the car, more or less.
Dealers don't care, and it's never once impacted trade in value. If someone says anything, tell them it's a GPS antenna, or tell them it's for improving cell phone coverage. Then charge them extra!