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Depends on setup, but frequently private keys are inaccessible to the web server worker process. (Which starts as root, loads keys, drops privs, etc.)

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Most popular ACME (Let's Encrypt) clients allow you to provide a CSR instead of generating the keys themselves. That means a bunch more work for you, but if you're worried about this, that's what you should do. Have your safe (even manual if you insist) process make keys, make CSRs for the keys, and put those somewhere readable. The ACME client will hand them over to the CA saying "I want certs corresponding to these CSRs" without needing access to your TLS private keys at all.

That does mean you aren't automatically rotating keys anymore.

If you trust your automation, you put private key rotation into it.

If you don't trust it your automation, you rotate the keys manually, as you would normally.

There are no valid reasons to throw the baby away with the bathwater.

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