Why couldn't the Navy be part of the Army?
Because some large ships take more than two years to build.
Typically, with such a large project, the purchaser will make a down-payment and sign an agreement to make payments on some schedule typically related to the builder's progress. A builder will want a commitment that the project isn't going to be abandoned before it's completed without some sort of severance payment. Absent such a commitment, a builder is going to want to charge so much up front for the project that once the bulk of the money is received the builder may no longer have much interest in its timely completion unless the government agrees to substantially overpay for the project.