As I understand the Licensing agreement from Paramount to ADB (I have not seen the actual agreement, but I am friends with someone who was peripherally involved on the Paramount side) ADB ONLY has rights to the "Star Fleet Technical Manual" ship era representations.
They contractually CANNOT use ANY OTHER Star Trek settings or official ships. They are free to create new ships that pertain to that setting but not duplicate anything in other series or movies (Including the upcoming JJ Abrams Trek Prequel movie).
If they were to publish anything that violated that licensing agreement, Paramount would be within rights to (And almost certainly would) revoke the agreement and sue both ADB and MJ12 for damages.
Star Trek is a hugely expensive license to obtain, as well, so I doubt they would have the $$ on-hand to re-negotiate. (Although Dan MIGHT be a secret wealthy billionaire dallying in the hobby. Who knows?)
PLUS we have to look at ADB's point of view. What good is licensing the game if they do not use the ship designs? The point is to help spur their Miniatures' sales, not just to help MJXII sell games. In order to do that MJXII will need to replicate the Ship designs at some level. HOPEFULLY this will be by massaging the Starmada designs to get the feel and general tactical utility of the original ship design.
If you are looking at this deal in the hopes that there will be "Official" Klingon Birds of Prey and Negh'var cruisers smashing NCC-1701-C it just ain't going to happen with this licensing deal.