concerning the wax stuff and salt/chemicals: i've never had any trouble with salt or chemicals in the chemical sense of irritation or anything. mechanically, rock salt isn't a whole lot of fun to run on, but i've never had anything irritate my skin. after all, there is at least a-little-bit-thick skin that it has to get through. conceivably, it can be troublesome in that you can have saltwater puddles that are below freezing but still soak you. but, i'm not sure how much worse that is that stepping in a normal puddle at freezing is to begin with.
concerning the seri boot thing: i think it is helpful, roughly as you outlined. sure, if you want to develop cold tolerance, you should probably be cold sometimes.
but, the baked feet do two things. most importantly, you will hopefully get thicker skin which then transfers heat less (out of you, into the snow/ice/road) and protects against pokies and chemicals more. second, while you are doing the baking, you will definitely have more blood pumping through your feet in an effort to keep the temperature under control. whether that results in overall better circulation or more/better blood vessels, who knows. still, for a few minutes, at least, the clean up crew and stuff will be moving around down there. and if you bake for a little bit, a little bit before you go out, you already have the blood vessels opened up and warm and pumping. my experience has been that they then stay open and keep things warm rather than the usual panicking that takes 4 miles to convince them to open back up again.
concerning greasy/mess/cleanup: well, no, you can't have it all. you want to keep the goo on the tops/sides (the back never seems to get cold...) and leave just enough room that it doesn't get on the floor while you're sneaking out the door. curling your toes toward the ceiling for a more duck-like gait helps on expensive carpets.
and it does tend to collect detritus during the course of your run. this means that when it's 10F and you turn that corner from a 10mph crosswind to a 20mph headwind, you *will* get some grit and goo on the inside of your backup shoes (although you can mitigate this some by bringing a washcloth with you or something to get rid of the major portion; or socks, i suppose). when you get back, paper towels are pretty handy. due to this, i usually only do it to extend the extreme lower end of temperature and wind before going straight to the moccasins from the get-go. i guess it helps a little with snow, but it isn't going to work miracles. to review: a) apply as close to the door as your small children will allow AFTER getting all your other stuff on/ready (maybe even crack the door open in case your fingers get greasy), b) prestage a junky towel and/or paper towels at the door for your return, c) plan ahead so as to not screw up your backup shoes, d) waddle like a duck with your toes pointed to the sky until you get out the door.