I'm gonna bet the contractor is charging you separately for replacing the rim joist. Unless you've written this type of work into your contract, it would not be reasonable for the contractor to incur the expense and material to fix such problems. You have to admit that you can't see through walls or existing siding, and tell what's underneath. It's very, very common to work these types of jobs separately. Not all siding contractors 'build' houses. One has to know more than just about hammers and nails and wood. THere are code issues and structural issues to know.
I suggest you handle this type of work separately because if you were to build something like this into a contract, you could end up paying an awful lot of $$$ for time and material that's never used. (Kinda like insurance.) My best to ya and hope this helps.