\My '93 came with Duncans, wouldn't change them at gunpoint.
Loves me some S-500s ...great guitarsI also love the PTB, but on my S-500 (MFD higher output singles rather than the "traditional" Legacy pups) I have to dial down the bass and treble as well as volume to get it into any kind of vintage territory. Bass goes to 5, treble to 7.5, and volume to 7.5 for a start.
I have '95 Legacy with a Lindy Blues Special in the neck .. Love it .. love it .. Lovvvve itI have a 1999 Legacy that I switched out the pickups for Lindy Fralin Blues Specials. I did not like the originals because, as the OP suggested, they sounded too modern. To clarify, I found them rather generic and lacking in the chime found in more vintage style pickups.
I got exactly that with the Fralins with no change in electronics. Perhaps the bridge affects the sound somewhat but, for the most part, it has a much more vintage Stratty sound.