At the end of the day, that's the same with all guitars. Is the S2 Cu24worth more than the SE Cu24 - after all the only difference seems to be a pretty veneer and multi-piece body vs being built in the US but still has the same PU's and Bridge. Is the CE24 really worth much more than the S2 Cu24 - the CE has US pups but has to go with the bolt-on neck - they both share the same bridge. Is the Cu24 worth that much more despite using a thicker piece of maple and the extra man-hours of sanding, using a US made bridge instead of the moulded bridge, coming in a hardcare, different neck construction etc even if they also use the same bridge as they do on the SE's. t gets worse of you look at the price difference from SE to Core - is the core really worth 4x the price? Do you get 4x the guitar?
I am not going to say that the price differences are worth it or not because for some people they will be and others, a SE, S2 or CE is good enough (although I hate that expression) for their needs/finances. There isn't a right answer and you know which model gives you the best bang for buck performance - the point that you don't get enough 'more' for the difference you have to fork out. You can look at Cars as a comparison too - the point at which version of the car gives you the performance, features etc and which options are not worth the extra in price. What you get for your money and how much you value different aspects, even money itself all play into the decision and why its not a one answer for all. If you are eaning mega bucks, $1k here or there isn't all that significant but to someone who may only have $50 a week free cash (after all their bills etc are paid) will find spending $1k on a guitar let alone paying $1k more, will have a very different opinion on what's worth it to them.
If you feel the CE 24 is the right guitar for you, that the Cu24 isn't worth spending extra on, then that is perfectly reasonable, Every tier of PRS are excellent in their price bracket so a great choice. Obviously used market may well be a way to get a guitar from a tier you possibly wouldn't of considered to buy new but the most important thing really though is to buy a guitar that you love to play and can comfortably afford. Buying something at you limit can be restrictive - not want to play it as hard or take it out to gigs in case it gets damaged and may not be as much fun as a cheaper guitar. As long as you are happy playing it, it doesn't matter if its not a 'core' PRS.