Now, of course, a lot of work went into ISPC and I'm very grateful, but mention in the docs of not being able to use the current stable release of nginx might have saved some time for us both
If you would have mentioned that you did not follow the guide would have saved us a lot of time indeed.
Supported in ISPConfig is what you find in the perfect setuo guide. Everything that you do not find in the guide is NOT supported. Using nginx from the nginx.org repo is not mentioned there, so its not supported.
Ubuntu has a include to the sites-enabled directory in its default confi and it runs under user and group www-data. There might be more differences as you get errors with the apps vhost as well.