So I successfully managed to get a high level example.com domain, and a home.example.com certificate for one machine that I have publicly available.
I now have another machine that I’d like a certificate for under machine.example.com.
Should this come under the other certificate renewal, and I copy the cert files to the other machine for use? Or should this machine make requests itself and manage itself?
There’s a security benefit in principle if each machine capable of getting its own certificate gets a separate certificate and uses a separate private key, because then, among other things, attacks against the individual machines don’t threaten the security of connections to the other machines. However, it’s not always the most convenient thing to work this way.
Can you use the DNS challenge method by updating the DNS zone? Then you don’t have to receive incoming connections on the other machine to pass the challenge.
So I used the DNS challenge yesterday to get the initial authorisation, would I just leave that in effect on my domain so that when renewal time comes it authenticates again?
You can continue to use DNS-01, but next time you renew, the random DNS record value will be different. Leaving your old TXT record in place won't allow you to renew the certificate.
You need to repeat the same process, including setting the new DNS record value, every time.
That's why DNS-01 is best when DNS changes can be fully automated, by munging .zone files, or through an API, or similar.