When you err in the other direction it tends to produce worse outcomes for everyone involved, with the mechanic often ending up eating the difference.
(I've worked as an auto mechanic in a former life)
A motorcycle that has been sitting for 2 years does NOT need a complete overhaul, as you point out. But there is much-better-than-even chance that the 1983 motorcycle hadn't had ANY major maintenance done to it up to the point it stopped being ridden. It was probably parked in the first place because it stopped running due to lack of maintenance. And everything the mechanic listed that needed to be done likely hadn't been done in decades.
My last encounter with a VFR750 involved a heat gun and a pry-bar to remove the carburetors, they're no joke.
[^0]: I love my GS1000G, but this wasn't my favorite part of getting it roadworthy.
[0] You might have a plastic reservoir with a screw-off cap, in which case... you'll use the JIS for something else.
P.S. Congrats on the new bike! Take an advanced riding course, read Keith Code, and buy good gear and you'll have a ton of fun with it.
Now, if he had recommended a full carb clean and battery replacement, of course that would bring the total to over $1000. Those recommendations are optional though, and your bike can live without them (if you enjoy using the kickstarter constantly ;)
As one who has made the mistake of buying a bike that had been sitting a few years, if someone asked me to ball-park an estimate, $1000 might begin to cover it. One might very well get away with less, but I wouldn't count on it for my estimate.
(And I've owned several Honda V4s over the years: those carbs do NOT come out easily, and they go back in even harder.)