Yep, and it's a damned shame, too... but the "overly legalese" rules for the contest led me to expect this from the very outset... a big part of why I didn't choose to bother with it.^If you read through those links he said there were also legal issues that prevented him from working more closely with Adam.
Legally, based upon the rules stated, Adam is not PERMITTED to work on the design that Cryptic is working on. He can work on something "similar" but the moment he won, his work ceased to be his in any way whatsoever. Cryptic/CBS have no legal obligation to acknowledge him in any way, frankly, and every time that they do, it's a potential "legal mousetrap" for them.
S&S's rules for the Titan contest were much less stringent... likely because nobody at "headquarters" really cared all that much about a ship called "Titan" with the chubby bearded guy and the whiny woman running it. (cough cough) But an "Enterprise?" You can just imagine the cash register sounds in their minds, cant'cha?
Adam gets some notoriety... and a free game. But technically, what he's working on now is NOT the "Enterprise F" anymore. It's something different, and entirely separate, from that. His involvement ended the moment he won... and as much as some of the guys at Cryptic may WISH otherwise, that's not going to change.

), but, you could perhaps "set" your ship a little further into Trek's future than Cryptic's. I doubt this war with the Klinks would last more than a decade, you could dub your enhanced design as the "movie refit" as it were; whether through enhanced energy transfer technology, or there no longer being a need to so heavily arm the ship, the refit could be seen by the design team as their chance to finally implement all the ideas which circumstance prevented during the original process.