Yeah it's also really subjective. The decision to score it an error is up to the official scorer. Obviously they have criteria to inform how they make those determinations, but it's still subjective.Fielding percentage is maybe the worst possible metric for defensive ability, because you can't make an error on a ball you don't reach. Put a literal statue at shortstop and it will only be charged errors for balls that directly hit it.
I mean, you're not wrong that Jeter was fine at short (most of the time anyway), but he also didn't do what was best for the team by insisting on staying there when a better shortstop was acquired. The only argument for not moving him to third and keeping A-Rod at short was that Jeter would be an even worse 3B than he was a SS.
Jeter was famous for those jump-throws in the hole which obviously were pretty and required a decent arm and good coordination. A shortstop with good range wouldn't need to make that kind of play. It's Torii Hunter Syndrome, where you make flashy plays because you're a "good" fielder but have shitty range or take terrible routes.
(I'm not shitting on Jeter by the way.)