/root/.ssh/authorized_keys

[Hyien]

What are the SSH keys generated by proxmox used for?
Is it safe for my config management scripts to overwrite this file with a custom one?

 

[Dunuin]

I'm quite sure PVE needs them.

 

[William Edwards]

What are the SSH keys generated by proxmox used for?

PVE Admin Guide, chapter 5.9

Is it safe for my config management scripts to overwrite this file with a custom one?

No.

Note that systems like Ansible don't remove keys if they don't explicitly have the 'absent' state. Also, you can add a file to OpenSSH's 'AuthorizedKeysFile' and do key management as usual there.