Well, since my comment seems to have grabbed some attention, I reference Mr. Smith of Annapolis who has said repeatedly that everything effects everything and that the pickups are a microphone of the guitar's natural sound.
I think it would be a fair conclusion to say that the classic singlecut style body of thicker mahogany and shorter scale length neck is going to naturally produce a different sound than that of the Cu24, whose scale length is longer...the mahogany is not nearly as thick (ever see the cross section of a Custom? The maple is about as thick as the mahogany at the body's thickest point). And the trem vs. the stop-tail is another BIG factor in the tonal equation.
I did not seek to deride the OP's new guitar, but I've read too many posts from Gibson fans who try PRS Customs and come to the disappointing conclusion that it fails to live up to their expectations as they relate to their Gibbys.
I admittedly have not had the pleasure of trying the new PRS numbered pickups, but I would guess (and I'm sure Mr. Smith would agree) that if you took the same set of pickups and installed them in both a Cu24 and a 58, one would hear marked differences in tone and, dare I say "girth".
I can hear the difference immediately between my McCarty and my SC245 (unplugged), and I'd bet the difference would be even more obvious between my 245 and a Cu24.
I'm glad to read a 'happy ending' story in this case, where a (former) Gibson owner is absolutely happy with his new Cu and St 24 guitars!
~Peace