Bringing this over from the Imperial Navy specific thread. It is my intended solution for ship limitations of ASC 2.0 ships.
I planned on leading off the ASC 2.0 with a foreword explaining that these ships are "unofficial" ship's, developed by the community for compatibility specifically with BFG:R. ASC 2.0 contains ships based off multiple sources, both official and unofficial themselves. As such, using these ships requires your opponents permission. It is recommended that these ship's be incorporated into fleets using reserve rules. How ever since certain classes may be impractical to include using reserves (such as BBs in smaller games) combined with the fact they are unofficial and already require opponents permission to use, players can feel free to use however many as they want in a fleet, though a rough 1 unofficial ship for every 3 official ships is still a good guideline to follow. However, players are encouraged to completely ignore any restrictions for special scenarios, campaigns or just plain fun (Unique character ships are still 0-1 though!) ASC 2.0 will also include some fun and fluffy but unofficial fleet lists. These lists WILL have built in restrictions and it is recommended that these be adhered to and other unofficial ships only be included using the reserve rules. Any special/rehashed scenarios included in ASC 2.0 should be followed as listed, but players are encouraged to modify and change up scenarios to meet their own desires and needs.
Bottom line: Everything is unofficial and meant for fun! There are some good guides lines that are recommended to follow for fair play, but if you and your opponent are up for it, anything is possible! ENJOY!
As for using the 40k allies chart, I think players can decide on their own whether to do things like that or not for campaigns/scenarios on their own, and it would prevent specific things in BFG like using Chaos ships as SM venerable BBs.