No, "all the problems from sitting" for 2 years should not include new brake lines, forks, etc. It does need just a carb clean and battery. Over-estimates are just as bad, if not worse, for a mechanic's reputation. He either did work that did not need doing, or simply said $1000 because he didn't want that shitty job.
$1k is a reasonable ballpark estimate for something like that sight-unseen from an experienced mechanic who understands how to manage expectations and prevent getting into situations where he's over-promised and under-estimated costs.
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)
I restore and wrench on vintage motorcycles. I also balked at first when I read this, but I think it comes down to bad storytelling rather than a shady mechanic.
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.
