You're paying a local pro GB for a very optimal setup of a $3000 axe... including taking care of everything needed such as a few high frets which are a certainty. On that level it's a no-brainer no? People pay $350 for $950 RGs they never saw before.
My own belief is that type of setup is better in a year or two (especially in 4 season climates like here) when everything sets, the wood dries/climatizes/settles. Good luck.
That's a shop setup, I love GB but he's not getting his hands dirty on your guitar. That's work for one of the 6 techs working in the shop under him. There's nothing wrong with the price though as long as it includes the PLEK, you didn't specify. And most likely there aren't high frets but the low spot in the center of the board between 12 and 17 that causes the most problems. A JS is tighter radius so if the fretwork isn't perfectly level you will get some choking points with really low action, especially in the second half of the scale where you have no relief.
$250 is what I charge for Silver which is everything, micro radiused, leveled, plus enhanced fret ends and board edge, plus the regular comprehensive setup, on a new guitar. Platinum adds $150, I never recommend it but I've done about 1000 of them and many just don't want any less, but that's full J Customized with 48 ball fret ends and very rounded board edge.
It's $350 for used guitars because they get a full breakdown and clean which always adds a couple hours, and with used there's almost always something that has to be debugged. Sometimes it'll be $450+ depending on what I see during the inspection when I list it, and some have taken 12 hours on the bench.
There is always a small portion of all of those fees that includes insurance for the inevitable accident that's always a looming possibility and with very expensive guitars the punitive compensation can easily leave you owing twice what you charged. Not like every shop takes the same approach, Simms [UK] sent back a brand new BRMR neck with the chrome vine that had 12 dents in the back of the neck. I don't know what you have to smoke to not realize you're putting 12 dings in the neck you're working on, but their "compensation" was to send it back, we'll fix it. Yea, they spot sanded them out and left the areas unfinished. So don't ever assume one shop will handle anything the way you'd want them to.
Not that I'll do any of that on your guitar as I quit ship in work a decade ago. I might sideline when I start cashing social security checks but the added communication is extensive, just the unpack and inspection is a process, so there are many added steps to ship in work that are never compensated.
I have no doubt there are decent techs that don't live in high cost areas [SF & NJ] that would change half those prices quoted. YMMV