I'll share an embarrassing anecdote hoping perhaps it will save someone else's misfortune:
I had a frame powder coated several years ago by a place that did lots of bike frames. The day I picked it up I was so excited to build my bike back up that it didn't occur to me to have the bottom bracket threads chased. There was not an obvious powder coat in the threads, but there was enough that it caused a lot of grief: I got the bottom bracket totally stuck in the frame and damaged the threads. I took it to a shop to repair the damage, but they had a lot of trouble getting it right. Ultimately they got it good enough to install the bottom bracket, but I worry about getting a new one in if the need arises.
Lesson learned: make sure the threads are properly prepared after painting or powder coating before you install your components! (Don't be like me-- Duh!!)