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My question is it possile to run vulnerability patches on the sec onion nodes? Or do those kind of things come bundled within each incremental update?

For airgap installations, OS updates are included in the latest ISO image. When you run soup, it will automatically install those OS updates from that ISO image. For more information, please see:
https://docs.securityonion.net/en/2.4/airgap.html#airgap
https://docs.securityonion.net/en/2.4/soup.html#airgap

Additionally, there was interest in running a STIG compliance checklist, is there way to access the underlying OS or would any setting changes compromise SO2 in general?

Security Onion Pro includes STIG:
https://docs.securityonion.net…

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@TheDude2741
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@dougburks
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Answer selected by TOoSmOotH
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