Yes, the roofer is going to warranty the facia, soffit, interior dry wall, flooring, exterior coverings, structural lumber and even the foundation. Really, they will. lol. Not going to happen.
Once anyone outside of the GC’s workforce and/or his/her hired subs do any work on that addition most warranties will be void. It’s just common sense. The roof has the ability to damage everything under it if not installed properly. The GC is not going to be liable if someone outside of his control causes damage. No court will enforce a warranty if there is potential third party liability.
Even if the GC agrees to keep the warranty in affect he/she knows it’s unenforceable one someone outside of his employ does any work to the addition.
I have no vested interest in the OP’s project. It makes no difference to me if a GC or stand alone roofer completes the job. However, there are pros and cons that must be weighed.
Here is my honest opinion.
If you are replacing just your roofing system. Find a roofing contractor (licensed and insured if applicable).
If your roof is being completed as part of a bigger project. Hire a GC and let them do their job. Or, be your own GC and manage the job your self.
The solutions above protect the property owner by keeping warranties intact , and assigning accountability to either the roofer, the GC, or individual contractors that you will manage.
Most contractors understand contracts and the laws that govern them. Some don’t.