I have, in the past, changed the color of some completed Bottlehead gear. I did not disassemble it to paint, though. The transformer stayed in place; I just masked very carefully around it. Tube sockets likewise, though if I remember correctly I removed the screws. Snap-fit items like the power entry module and the power switch were lifted slightly from their installed positions and masked around but not disconnected.
I gave it a very light sand to prep for paint, cleaned with compressed gas, a vacuum, and then an IPA wipe. I used the masked base as a stand for painting. All in all, it was a straightforward task and not that time-consuming.
If I remember correctly, it was my SEX 2.0 that I repainted; can't recall what color I changed it from, but I think I wanted it to match my Paramounts, which I'd painted in a kind of antique gold finish. I've since switched all my new builds to mostly dark charcoal (almost black), black, or silver (clear painted standard BH finish), following the two poles between which audio fashion seems to swing. If it's something I'm likely to keep a long time, I go with charcoal/black. If I might not keep it a long time, I go with silver.
I mention all that because now, years later, when I look at my SEX amp or my Paramounts, though they look like nice antique-gold things, they appear hopelessly dated. When I look at my black or silver items, they just look like audio gear. Makes me wish I'd heeded the Rolling Stones, and decided to "Paint it, Black."