I'm not sure why though, because Ploi doesn't use SSH keys to deploy or clone from, it uses oAuth tokens.

Or am I missing something here?

Yes, this isn't related to how Ploi clones or anything else directly. It's just an easier way to distribute SSH keys when for example rotating them or adding a new machine. Just upload them to GitHub as "single source of truth" and they are automatically synced to servers to allow SSH access for myself.

Does this help?

I think I get it, so the keys present in your GitHub account, do you want those synced to your servers?

Exactly.

That's quite interesting, I'm not sure we'd automate this, but a button near the Source Control provider for Github to import those, would be a good start I recon?

Yeah, this would already help.