I think some of your expectations of what will be detected on an audit are slightly overblown. A 3rd party audit, as they're at pains to point out, is only a sampling exercise.
Would I expect someone to write notes as they're doing tests? No. Would I expect where results are recorded to be prevented from being altered (whether electronic or hard copy)? Yes. Recording test results and nothing else doesn't mean undocumented in my view but interested in others. Some testing doesn't require you to take notes. It depends a lot on the test. You've not shared that so it's a bit difficult to know.
Would I expect good document control? Yes and I'd expect lapses to be detected as that's easy to spot.
Would I expect some document security? Yes but that would be easy to hide if it were poor so I'd expect an auditor might miss it. I know of few auditors who check this well.
Do I expect documents to be signed? No. Electronic approval is fine. Ink signatures are not required.
Do I expect follow up on efficacy of RCA? It's good to do and in theory required but in practice, most sites are so poor at doing RCA, if at all, that's unlikely to be something you see widely in the food industry. Should we do more of it? Hell yes but most GFSI auditors will miss this or not raise or rather will only obliquely raise it. For example, if you have a rash of repeat incidents despite RCA, it proves the efficacy of your RCA was poor which is probably more direct in proof of your failure to assess efficacy than having a record of that check.
It depends what you mean by inspections. Monitoring for HACCP should have clear criteria. GMP audits or similar should be structured to a degree, audits the same but there needs to be freedom to record what you see and not tie yourself up in a tick box mentality. There is benefit in following your nose with auditing of "that doesn't look quite right." In that way, requirements CAN and SHOULD change on the fly according to what the risk is.
So out of your list, I would expect an auditor to raise if records can be altered and if documents are not controlled. The remainder, I'm not sure that your focus is risk more that it's compliance. The two are not the same.
BUT should you spot all of the above on your internal audits? Yes you should, if the points are all justified, e.g. if you genuinely need notes being taken in the lab for example. Your internal audits should be 10x tougher than the external as you have more time over the year to do them.
While I don't think all of the gaps which you're shocked by are really all that bad, I stand by my previous comment that auditors in the food industry are not well paid, are hard to find and are not (sadly) treated to first class and fine dining. Some CBs who contract in staff don't even pay for travel time believe it or not even when you're travelling internationally and cannot "sell" that time to anyone else. You get what you pay for. But also there is a level of pragmatism that SHOULD be there for all auditors. When I audit as an external consultant, I'm looking vs. the clauses but my main focus is always where there is risk that's present now or likely.
Also...
It doesn't appear you understand auditing and Quality if that is what you think.
Bad day?
Trust me I think everyone has told me I'm lacking in some area of my fundamental faculties on here as a professional or as a person at one time or another. I know I can be an intransigent curmudgeon at times. But we're all here to help and because we're passionate about food safety and quality at heart. We're not the bad guys.
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