Master cylinder questions

I've "bench bled" them while in the car without any problems at all. Just be careful how fast you depress the pedal of you can have a big mess and more than you bargained for in the paint removal category...lol. With the hood up you can view it between the hood and cowl until all the air is expelled. I place lots of rags under that section of inner fender just in case there's a spill over.
I've never seen an aftermarket stock type MC painted but have used WD40 on a rag and wiped it every so often to keep that cast looking fresh. Not sure if that's the best method but it's one way.