They can indeed charge whatever they want, since you can't make a Gibson style guitar without getting sued. So if you absolutely want that Firebird V, 355, SG Custom etc., you'll go for them, since between them and the Custom Shop there's nothing.
Having looked around a bit, it seems that the guitars have the 'inspected by Epiphone USA' sticker on the back of the headstock, which has featured in the past on various models, and goodness knows what that means in practice. I saw a teardown of the SG Custom and it had bad frets and the usual Gibsonesque tooling marks on the binding, so at least on that one, fit/finish isn't better than usual.
I also wonder why they're putting linear taper pots in everything. When I got my IbG SG Special, I thought it was a bit odd, but since then have seen that everything else from IbG to IbCS and the signatures seems to have them.
The Custombuckers seem to be the most notable component factored into the upcharge. Other aspects of the hardware and wood, I don't think as much (as an example, Zzounds is selling a sparkly flake SG Custom which has full binding, ebony, mop inlay, Grovers, for $629).
People talk about the laurel fretboards a lot; for Epiphone, it's arguably a savings measure, which isn't passed on to the customer, and I guess this is where some of the beef is coming from, since there are other guitars in the similar price range and sub-1k which do use rosewood.
