In 50 years of shooting BP, I've only had one flash cup on one of my rifles - and that's because it came with it. It was on a H & A underhammer that I purchased new from Deer Creek. The only reason it was on the rifle was because of he close proximity of the nipple to the wood forestock. To be honest - I hated it. As stated by another it was a PITA. I finally removed it.
I've never used on on any of my side-lock rifles. Yea - after years of use it might show a little on the wood around the lock - but I have yet to examine an original rifle that saw extensive use that didn't show the same things - I jsut call it "character".
I got to the point where I use one of Ted Cash's cappers most of the time - I couldn't use it on my underhammer with the flashcup installed and I doubt if it would work on a sidelock either - maybe someone out there who uses a Cash capper and has flashcups can speak to that?