My R01 application was re-assigned to a study section that doesn't seem like a good fit (NIH)
I think the problem is that you "misunderstand" the sections, and whether that is right or wrong, you have to change that perception.  I have a PI with a similar problem, and she decided to resubmit and "play along".  R01s are hard to get funded when you're new.  Plan on that  -- average age of new PIs in the 40s -- not 30s.  That said, I would say if you can ask for clarification (playing coy), that might be your best option.  The PI I support said, "we had X-topic expert on our proposal and they still said we didn't have enough expertise on x-topic!"  Sure, she could misunderstand what expertise in that topic looks like, but I think in general, if she wants the funding, it behooves her to ask the relevant NIH person more specifically what expertise one needs to be convinced that this PI knows what she is doing and how to get the proposal funded. Sometimes you have to bend (who you include, how you write them in); other times, we have to convince the agency.  Do your docs help convince the agency of your POV?

In general, I don't advise faculty to antagonize the PO, but they are supposed to be the public face of a program, and they should be able to answer some of these questions.  Asking questions about submitting is not too much.  That is the job of the agency, to answer your questions on the application process.  Forge ahead there!