I think its more about separating more from the SE Line which has been on fire in the last few years - Probably since bringing the Paul's Guitar to the SE Line and that 'Core' Bridge, then the SS's, HB's and 594's too, the SE line has been on fire and therefore, the 'American' built S2's probably were suffering - why pay a bit more when SE's are so good and if you're thinking you 'need' to swap out the Pick-ups for their US equivalent (or other Quality expensive brands) on an SE, then you'll think that too about the S2 line.
The US Made Guitars will now all come with US made Pick-ups by PRS themselves - the price has gone up to reflect that, but it also separates them more from the very successful SE line. therefore It maybe does marginally move the Gap between the S2 and Core slightly narrower, but from a manufacturing perspective, it doesn't change any of the 'costs' or 'hands on' time in making each S2 Guitar. it costs the same to install whatever pickups/electronics into it during assembly so its just the 'extra' costs of parts which are made in factory (no shipping from Indonesia for example adding to the costs of using overseas parts). So its still the 'same' design philosophy behind it, still not a 'Core' and still the most affordable US made PRS line and now is more US made that separates it more from SE's than moves it significantly closer to Core