Just did a couple for a company that dies not do re-work, doesn't have compressed air etc. Each one also gets a standard statement - should the facility decide to use compressed air we will reviee the standard and create documentation, procedures, testing, etc to support SQF code/# etc.
These get inserted and that way we keep yhe code sequence in order and the Auditor does not get hung up on asking where is such and such.
I bolded what seemed most important in my experience. By not mentioning something in your own program because it's not applicable, an auditor would say you're failing to acknowledge it should it someday become relevant to your business. You can absolutely write a separate document with all the non-applicable codes, or you can put statements into your existing programs near where the non-applicable is relevant.
First FSQMS I helped write for a company's first SQF audit, we too only used compressed air to power some pneumatic gates and plungers, and there was no risk of air hitting the food. We opted for an annual air test to avoid trying to totally exempt ourselves from the code, but the risk analysis stated low risk due to no food contact so the annual air test was fine. We wrote in our EM program that should air become regularly used, we would update the risk analysis and increase air testing.