I have been through most of the variations of buffing setups around at one time or another, both buffing handmade knives and now pens. And to be honest almost all work pretty well, from the basics of a cotton buff on a bolt mounted in a drill press, to a 3 buff system running on a vs lathe. The single most important thing to keep any buffing system working well is keeping the buffs CLEAN!!! The buff on a bolt thing with generic compounds from sears will produce a better finish than the most expensive multistep setup available, IF the buffs on the multistep get dirty!
So, the question, IMHO, is not so much which type of system does the better job, but "which system is easiest to keep clean" The best way to keep a buff clean is to keep it sealed in its own separate ziplock bag until you are ready to use it. Then do a quick sweep of the buffing station with your DC hose or shopvac, and then mount the buff. So, if you want the very best results, a quick change single buff solution is my recommendation. Now if you just have your heart set on a fancy multiwheel system, take some time and think about how you are going to keep it clean before you get it. Cause once it shows up, you are going to have to do "just a couple of pens", then something else will happen and by the time you get around to doing something, the buffs are already contaminated. (that's the way it always seems to work out for me, anyway). As for what to do, that really depends on your setup, but for most folks where the buffing station is in the shop with everything else, your best options are to either have a fairly airtight enclosure that can be placed over the entire setup (best) or a permanent enclosure somewhere nearby that you can hang the buffs in as soon as you take them off the lathe. You want the buffs to be able to hang without touching anything if possible. The last solution, which I don't favor because it requires the user to remember to do something every time, is to use some sort of individual cover on the buffs. A plastic grocery bag put over the buffs and tied underneath will do just as good a job of keeping stuff off the wheels as a fancy sealed cabinet, until you forget to put them on that one time and fire up the lathe or the tablesaw or whatever.