Specifically, what do they do wrt. pre-purchase assessment and boot selection, and then post-purchase modifications, that other less-knowledgeable bootfitters don't do?
Pre-purchase, it doesn't look like they do much. They'll check out the size of your ankle and lower leg, to select a line of boots for you based on the hole size, and will then use a Brannock device for sizing length and width. A good bootfitter will know right away which boots would be good fits for you (hole size is primary, then width and flex), and a brief conversation about what kind of skiing you do or what flex you're looking for will get you to pretty much the exact boot you should be in. If it's a retail environment, he'll probably bring out another option so you feel like you're making a decision, and not just doing what you're told.
Post-purchase, there's a menu. Casual purchasers may walk out with a boot that'll "work fine" for them out of the box (meaning they won't know what they're missing, don't want to pay extra to find out, and will leave happy with a boot that just fits well). If you're more performance-minded (this would've come out in the pre-purchase conversation), you might have been encouraged to buy a narrower, lower-volume boot, which would include the expectation that it would be widened to fit your foot and had plastic ground out to fit the knobby oddities of your particular feet. There is also a budget consideration.
If you're paying for a full setup, like you would if you were getting into a plug boot, to include alignment, etc, the process is much longer. In that case, as soon as you buy the boot, he starts cutting stuff off of it. He'd widen it to fit your foot, grind out the bootboard and interior so your foot sits properly in it, grind out whatever hot spots you detect in the store, probably cut down the cuff to suit your lower leg (or at least to get the plastic out of the way of the power/booster strap). He'd talk about footbeds, and whether you need them. If you need them, he'll make them. Aligning the outside of the boot without doing the inside first is a recipe for disaster. If the footbed conversation includes key phrases like "you pronate, so you need a posted footbed to support your foot", run away. "Correcting pronation" is also known as locking the foot in the boot so you can't use it. The pronating feet that need to be "corrected" are the ones that also have a twist in them, and it's the twist you want to address, not the pronation. Rigid footbeds are a sign the guy doesn't want you using your foot inside your boot at all, so I'd recommend avoiding them like the plague.
Alignment is handled differently at various places, as well. For it to work right, each boot should be aligned individually so you can stand on one foot well, and it will then work fine with the other when you use them together. Your alignment should be confirmed on snow. Your fore-aft setup should be checked out on snow, too. Skiing includes a lot of dynamic fore-aft movement. It's not a position you want, it's access to a range of motion, and for support to exist where you need it. Your conversation with your fitter should be in these terms.
The biggest difference is really that a great fitter fixes causes, while the other guys treat symptoms. A perfect example is one I ran into when I first got my Head Raptor 130 RD's. The shop I bought them from was highly recommended, etc, and were very interested in making them work for me. I spent probably 4-5 days going back and forth between the shop and the hill, finding new hot spots and problems, and them grinding them out. Well, one problem that never went away was that my big toes always hit the end of the boot. No matter how much room they ground out for me, my toes always filled it. I eventually gave up on this problem (there were a series of others, as well) but, when I went to see a great fitter for a second opinion on the alignment (thanks to recommendations on the PMTS forum), he fixed my big-toe problem instantly, without my even mentioning it. He pointed out that the boot had a 95mm last, and my foot was 98mm across the met heads when weighted. Because feet and boots are both shaped like V's, the bigger V of my foot was always going to rocket to the end of the smaller V of the boot once I weight it, because it's seeking a width that'll fit it. He widened the boot by a few millimeters, and my big-toe problems went away.
Fix causes, not symptoms! It oughtta be a mantra..
Anyway, I hope this helps a bit. I'm no expert or anything; I've just had my share of problems and spent a bunch of time hanging out with a really, really good bootfitter who's been absurdly generous about answering my questions and showing me stuff.