If you take the waxed chain somewhere where flakes aren't an issue (say over an open newspaper in the garage) and work the chain a while, most excess wax should fall off. Or, prop up the rear end and spin the pedals for a while and the excess should flake off.
If the flakes stay on the cassette, it is no issue for me, but if it bothers you, get pretty much any kind of brush and brush them off.
I use paraffin and PTFE powder. Way cheaper than MSW and pretty much exactly the same ingredients except for the anti-caking agent which I don't need since I don't have the stuff sitting in a warehouse for two years before being sold and used. I mix up a batch whenever I need and it lasts a long time. Using 6-micron powder prevents all the PTFE from dropping out of suspension while cooking.
As for the "clean drive train," the benefit isn't so much the appearance (which is a lot cleaner in my experience) but in that you don't have a thick, abrasive slurry of old grease and grit eating away at your chain, cassette, and rings. Everything lasts longer with waxing.