MCE, your correct, doing the bottom is the easiest way, I have also done it in my CBN tooled Serdi head/deck mill on the top but you have to take extremely light cuts to keep from "smearing" the aluminum. The lathe with C-30 or better carbide cuts the bottom OK, ya take a few cuts and resharpen. I don't know if a normal human could wear those cylinders enough to ever need a freshen up. After a year or two you just don't see any wear, pretty much the crosshatch the way it was when new.
I have talked to friends at Total Seal (they are local) and they sell what they call "Fairy Dust" , its a diamond lapping compound that is applied to the cylinder walls during assembly to aid in breaking in the latest crop of harder than PHX. in the summer race/ blown/nitrous rings. Great idea, but I can't get past the idea of putting diamond lapping compound into the rest of the engine. OK for a race car that gets torn down often though, I guess.
Those cylinders have been completely trouble free in every install we have done, and we have been using them since they came out. We don't sell anything that we haven't personally tried in our own scoots.
Headers on my CVO Breakout are Patriot Performance stepped 2 into 1s with heavily modified baffles. We also use the Drago's stepped headers too, and prefer those as they are coated inside and out, but Frank doesn't make the Dragulas for a Breakout. The Patriots are a bit longer in the primary length too, and I like that, but it would look ridiculous with an actual long enough tuned primary tube. We have our local guy do the coatings, he is great! P.S. we get the pipes coated inside and out and also the inside of the heat shields too. Motor temps will run lower with everything coated, at least here in Phoenix,AZ. TIMINATOR