Absolutely! I don't know how they do it!
Explains why this is a $1k guitar. Obviously there are some areas that no doubt keep the costs down - using standard size Pick Ups mean that those that make them, aren't having to also make new 'raw' parts specifically for this model. Having seen the difference in size that the pick-ups are - longer and slimmer - that no doubt reduces the costs.
Its possible that this guitar isn't as lucrative to PRS as say their Custom 24 SE. The profit margin being a lot lower because they feel it can't be sold at more than $1k - feel like the market can't and won't accept an SE costing more than the lowest price(s) of the S2 range. There have been comments here making comments about the price and its proximity to the S2 prices - even if it is the most 'basic' S2 which has more in common with the much cheaper SE Standard models. Some people seem incapable of comparing 'like for like', a Custom 24 SE with the Custom 24 S2, with the Custom 24 CE or with the Corse Custom 24. I know there is no S2 or CE 'Paul's Guitar' but you know if they did, the S2 version would be very close to the CE prices and the CE version would be very close to the Core prices. I know Epiphone has some models above the lowest priced Gibson Les Paul (at least they did the last time I looked) but those are generally the signature models. I also don't think many people really give much thought to the Studio range - you barely hear people mention them as guitars under $1k.
Having seen inside the back of these, at the electronics, there appears a small PCB so I believe that plays a part in the TCI pick-up splitting. Another aspect, relating to the SE and the sizing is that these are also the Pick-ups in the new SC Santana gold top. The fact that these are regular size means that they can be used in any humbucker guitar - whether they use them just as a Humbucker like in the Santana SC or as a splittable Pick up like in the Paul's. If they wanted, they could use these in any SE build without having to change the routing. That must help reduce the prices of the SE Paul's too - spreading the costs around other models rather than just making one-off's for a specific guitar.
In my opinion, I think these guitars are very competitive with others in their price range. At the end of the day, that is most important. $1k can buy a LOT of guitar these days and if the Paul's was 'over priced', that people can buy something significantly better - not just in versatility but in playability, and tonal quality, it won't sell - well maybe just to a few PRS fans who then complain its not as good or worth the price they paid. However, the two video's I have seen comparing the SE to the 'Core' Pauls, a guitar that costs 4x (or more), its performing admirably. If I was in the market for a guitar under $1k (or under £1k as I am in the UK), I would seriously consider the SE Pauls in Red (of course). At the moment though, its not on my radar as I am gassing for a Special 22 and a 594 Hollowbody....