I would have thought that you have the basic rules of playing a miniatures game ACTA style available, but if you wanted to add your own ships, weapons, etc then you make up your own (or more likely borrow someone else's). Tournaments / Clubs will have a pre-agreement about the rule sets that they are using - so if you don't like their Gaim variation - tough. Find another club or start your own.
A simple example would be that anyone can produce a set of fleet lists for use with Star Wars, based on the ACTA game mechanics. Whilst there may initially be 100s of different variations, some will become more popular than others (based on fairness, consistancy and perceived accuracy). The most popular fleet lists may even get published - but not necessarily by Mongoose.
So to answer 2, I would expect to find submarines in the appropriate fleet list book, but not the main rule book.