Given the significant updates to the S2 Custom post 2024, I'd be hard pressed to take a Core over an S2 if it were to be a working/gigging guitar. I'd feel a lot less ticked off to get some bar/club bumps and bruises on an S2 as compared to a Core. That said, I have and have gigged both S2 and Core guitars. I have both a Core 35th Anniversary 24-08 and a 10th Anniversary S2 and when comparing tone for full on bridge and neck pickups, there's no discernable difference in sound, especially when you're competing with a drummer, bassist and vocals. Sitting alone in my music room, there still isn't much if any gap between the two when you're talking full on humbucker.
As to whether the cost of the Core over the current crop of S2 is worth the premium, that's up to the individual. I've had plenty of really nice guitars that have scarfed necks, including late 90's Japanese Ibanez guitars and have had no issues with the them when compared to my Gibson and Core PRS guitars that have quarter sawn necks.
Some of the other considerations when deciding Core or current S2, however are also the S2 locking tuners versus Phase 3, and the different bridge. The S2 having the same bridge as the CE and SE guitars (molded bridge with Steel block and saddles for the S2 vs machined bridge with brass block and saddles for the Core). Does it make a difference in tone, maybe, but not enough for my ear to ascertain. There is also the difference in inlays, while the 10th Anniversary S2 had mother of pearl, I think that even the updated S2 line is back to using the plastic ivoroid inlays. Does it make a difference other than aesthetic, no, but for the sake of vanity, it may make a difference to some.
S2 is a tough line to beat now that they share electronics with the Core guitars. It's similar to the gap between the Gibson Les Paul Studio and the Les Paul Standard or Custom in the late 90's and early oughts (i.e. before Gibson was using a push pull pot for each volume and tone knob and wieight releiving and relief carving the neck joint on the Studios). It's a question of how you want to spend your cash at the end of the day.
