Multiple instances sharing one codebase

I currently have two 10.0.2 instances sharing DB and storage on one server without an issue, though the inbuilt theme engine updates all instances, meaning I’m having to rely on the “old” theming method in order to theme each instance separately (the goal of this experiment).

I was looking to see if I could share one codebase across instances with only .htaccess, themes and config being unique in directories, the rest being softlinked to a central NC folder:

This however did not work, as it insisted on using the config from the source location and ignored the local files within the directory :frowning:

Am I missing anything obvious here or is it simply unstable due to being an unsupported installation method?