Any way to have Safari/Keychain autofill password on a single site with prompting on all sites?
I'm not sure if this workaround will suit you, but does the site in question offer a "Remember me" type option? If so, you could just manually log into that site and tick the 'remember me' option so that you don't need to log in again.

Assuming the above works for you, then you can keep using your password manager as you do now and also avoid enabling Safari's password autofill function. You can then keep this workaround in place until your password manager supports the site in question.