You don't have to take the system apart to "wash" it out. Open the bleeders and start pumping! Keep the MC full of alcohol until the system is flushed. I usually flush one end (front or back) at a time. MAKE SURE you have pure alcohol coming out -- refill the reservoir at least twice, and three times won't hurt. If you have traces of the old brake fluid in the lines, calipers, or wheel cylinders the silicone will gell when it mixes and clog a line, causing a wheel to stick. The slightest amount will do it! You can run the silicone fluid in a DOT 3 system, just don't forget to use silicone only!!
I've flushed brakes several times using the above method with no problems. I usually refill the MC twice, then go back and flush half a reservoir of alcohol through each brake separately, just about like bleeding brakes, just to make sure noting was left in a line. Sometimes if a line has a partial blockage, but not enough to notice, or one short and one long line (like a T feeding front brakes -- the one nearest the MC has a shorter line), the line with the least resistance gets most of the alky flushed through. By going back the final time and flushing each wheel I make sure every line is clear.
Unless your car sits a lot between drives silicone just isn't worth the trouble. Regular brake fluid won't hurt paint as long as it's washed/wiped off immediately. If you want to paint the MC it's a problem because some will seep under the cap seal, but that's about all. A powder coated MC would fix that, but you need to take all seals out before having it powder coated. If it's a brand new MC an epoxy paint, with 24 hours cure time before use, should hold up. Make SURE the MC is THOROUGHLY CLEANED before painting or powder coating. Clean real good with paint thinner or mineral spirits.