What exactly do bootfitters do? I know they fit boots but how exactly do they do that?
They'll look at your feet, your arch, how wide it is, how you stand, the angles your feet are at and all that (I'd make a longer list, but I'm NOT a fitter).
Any fitter worth anything will be able to tell you what will most likely work best for you. For example, you come in and tell him you're getting pain on the sides of your feet after a run or two. He looks at your foot, has you stand up and walk around while he boserves, and tells you you've got a wide foot (an arbitrary example). He knows Salomon boots come in wide sizes and Northwave boots tend to suit wider feet better. He can tell you that Vans run a size small (I'm 14 street shoe, 13 in my Vans boots).
If you've got arch problems, he can sell you new insoles or in extreme cases, custom make an insole (which is what I have.. best $175 I've EVER spent.. except for those hookers that one time in Tijuana).
And why do you go to a fitter and spend full retail on a boot? Because he's given you his expertise, and he will stand behind his service. If you walk out of there with a boot and find it still hurts, he'll work with you to make it right.
You can have a Burton Vapor ($1500) and C10 bindings (I don't know how much those are) and their most insane $500 pair of boots...... What does it matter if your foot hurts so bad at the end of one run you have to take a break? The guy with a Lamar shit-stick and Lamar bindings who went to a boot fitter and laid down good money is taking 15 runs a day without missing a beat. Who's having more fun?