The pots, switch and wiring are all the same as used on the Core's, so the only difference in electronics would be the pickups themselves. S2 Thinline has 58/15-S pickups (made overseas). Closest equivalent to PRS Core that you can buy would be the 58/15-LT, although those are spec'd slightly differently than the "S", they have fewer turns of wire, resulting in a lower-output and somewhat warmer sound.
I have a Thinline, and am perfectly happy with the S pickups that it came with (FWIW), and upgrading to the LT's would cost around $500. Of course there are a ton of other brands that folks love that would cost you less, but you specified PRS Core standards...