Charge for TT setup?

I'm upgrading my TT and am looking at a VPI Classic 3 which retails for 6K. The dealer wants another $100 to take the cartridge off the old table and put it on the new one.
I'm thinking at 6K set-up should be included but I'm not very knowledgeable. Is this a standard practice? Or is it free only if I also buy a cartridge from him?
Expecting your ass to be kissed is ridiculous, no matter the margin. That's not a good way to live life or conduct business. Be a reasonable human being. However, in this case you can expect to have the upper hand in bargaining, and use that to your full advantage. A discount plus free (quality) installation can be had from other dealers; prepare to walk if this one won't budge.
It's negotiable. It's a business transaction not armed combat, so don't take it personally. I assume you're talking about in-home steup. If this is the turntable you really want, don't be so quick to walk away in a huff. You're talking about $100, less than 2% of the transaction price. Between the in-home service and some analog accessories (cleaning brushes, VTF gauge, etc.) the two of you should be able to come to a mutually satisfying agreement. The dealer makes a nice profit and you will have years of analog happiness.
In the late 1980's, I bought a Sumiko Bluepoint from Overture Audio in Ann Arbor, MI. The cartridge cost maybe $250 and they mounted it for free as was typical at that time. They spent about 2 hour doing it because my they had to have alignment templates faxed from Magnapan for the discontinued Unitrac arm I was using at that time.

Not surprising, with that level of service, that brick and motor store is still in business.

If your buying a $6000 turntable cartridge setup should be included. Even the online retailers will set up the turntable for you prior to shipping.

Now if they have to come out to your house, I think that's a different story. I once paid $100 for someone to come out my house to repair a broken phono lead and he also setup the cartridge. At the time, I had a VPI TNT which is not a turntable you just put in your car and carry into the dealer.
The OP's dealer is either begging to go out of business or agorant enough to think he's the only vpi source.

Doesn't a 40% profit margin mean you are supposed to receive value for that money? Isn't the argument that brick and mortar stores is that they provide service? This guy isn't.

Walk away and watch him come after you.
Given the typical disposition of us audiogon forum goers, "years of enjoyment" is much more likely to be: "days of bliss, followed by months of tepid satisfaction, giving into doubt, followed by days of increasing upgrade urges, finally culminating in a new 'what should I buy' thread" ;)