I think its clear where the 'extra' money goes as you move up through the different ranges. From the SE Standards to the Core lines, its clear why there is a Price difference to me - That being said, I don't necessarily think there is a massive difference in Tone or Playability. The Custom 24 is a model in every price range - from an SE Standard and Custom to S2 Standard and Custom to Core and beyond. Each is a step up - whether its a solid Mahogany body, Mahogany with Maple cap and veneer, to mahogany with a flame maple cap with no veneer. Then you have the different top carve with the Core being the most sculpted - the advantage of using a solid maple cap without a veneer. There are also differences with some having a bolt on neck and obviously some of the necks are 3 piece necks too. I know you could say the headstock of a core is 3 (or 4 if you count the veneer on the front) as they add 2 wing tips but still carving the heel and majority of the headstock out of 1 piece of wood is more expensive than making it out of 3 pieces - they get more necks out of one block of wood with a 3 piece construction.
You are paying more for the core also because it goes through many more Quality control checks too. The SE's are built abroad and shipped to the US where they are checked once. I don't know if the 'woods' in the SE models are checked as thoroughly or selected as vigilantly as the US models, I don't know whether PRS grade the Mahogany for example and use the 'best' for the Core and above models but we do know they do keep the best Maple for 10-tops and the 'very' best for PS/AP models. It would be interesting to note how long a guitar takes to build from receiving the raw wood to leaving the factory. Core models take months but I don't know how long the other models take - which again may affect pricing.
You also have to consider that US labour as well as factory running costs (electricity, rates etc) are much higher too so even Kiln drying will cost more than places like Indonesia or Korea where the running costs are much lower.
At the end of the day though, everyone can afford a 'PRS' - whether its a core model or SE. The tones and playability are superb and as we know, many 'professional' artists will happily gig with SE models. Of course certain models may not make it to SE - like the 509, 408 etc but maybe the 594 could as that seems incredibly popular but, like the Silver Sky, there are a lot of similar alternatives - like the Epiphone LP or Squire/Mexican Strats. Anyway time will tell...
