I thought there were more carbon than standard bikes, about 55/45 split, but it's not important.
From the BMW Mottorrad website for the additions the carbon has over the standard bike:
"HP brake lever, HP clutch lever and HP rider footrest system. The long, closed HP engine spoiler, the HP plate holder and the HP fuel tank trim are made entirely of carbon. Its most conspicuous hallmarks are the aluminium forged wheels in Racing blue and the sponsor sticker kit - so its unique quality lies not just in its performance but in its design, too, making it a perfect synthesis of quality that is impossible to miss.
The HP4 Carbon also has the consecutively numbered fork bridge engraving with HP logo. This makes each and every machine a unique specimen."
Performance wise they are the same.
The carbon will always be more desirable on the resale market simply due to the sum of its parts. It will also be easier to sell for the same reason.
Will you get the premium back between the models? Maybe. You'll get more for the carbon v standard, but as much as the difference you pay up front, who knows? I guess like with everything it is supply and demand.