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It's a security thing to avoid *unknowingly* installing vulnerable versions of macOS. Apple ultimately wants you to give consent to remove your machine security *through* a trusted environment to begin with.
There is no requirement nor *way* of phoning home to ask about any specific custom kernel or OS. Apple doesn't know what custom kernel you put on your machine, or that you disabled security. All they do is certify that your initial/bootstrap macOS install was up to date.
