if i sign a contract to have my roof and siding redone due to damage, can they only agree to the roof and not the siding costs that insurance will pay

The contractor is not bound by the estimate your insurance company got.  As you probably noticed, the adjuster was using software that came up with a number.  Your contractor probably uses the exact same estimating software, but is not required to bid the same amount. You may want to try getting a bid from another contractor.