There's a missing part here, and that's validating your ACME account ownership.
I think most users depend on automation that creates their accounts, so they never have to deal with it. But now, you need to propagate some credential to validate your account ownership to the ACME provider. I would have liked to see some conversation about that in this announcement.
I'm not familiar with Let's Encrypt's authentication model. If they don't have token creation that can be limited by target domain, but I expect you'll need to create separate accounts for each of your target domains, or else anything with that secret can create a cert for any domain your account controls.