Powder coating, plugging threaded holes

A. If the part was never taken apart and was not subject to vibration, your method might work, but I would not be keen on buying the product if I knew about it. Your competition could have a field day with it.
Silicon pull plugs should work fine.

A. I've been involved with that process before, it works well as long as the painters have good control over the thickness of the paint. If the paint gets too thick the holes have to be chased with a tap.

A. I've used nylon screws in threaded holes prior to powder coat.

If your desire is not to mask the holes keep in mind that the thread pitch diameter will decrease by 4X the powder coat thickness. So oversized taps are required. Generally not the most reliable technique because the powder coat thickness varies, especially inside a threaded hole.

A. I purchased a set of American Torque Thruster wheels that had been powder coated but the threads were not protected (covered). Powder coating is very hard and will quickly dull a tap.
Highly recommend you acquire a tap and drill chart to determine the correct drill bit to use. In my situation the threads were 8/32nd NC which requires a #29 drill bit. Pre-drill the threaded area to remove some of the powder coating, then use a threaded tap (8/32 NC, National course) to remove the remaining powder coating and essentially clean the threads. If you don't pre-drill you could easily dull a tap quickly or potentially break-off a tap in the hole. Then you have a real problem.