I explained myself badly.
Git as GIT_DIR and --git-dir for specifying location of the ".git".
What would be nice if there was also something like --git-dir-alias or similar for specifying non-standard name for that directory.
Then I could along the lines of
git clone <project URL>
cd <project>
export GIT_DIR_ALIAS=".git-private"
git init && git remote -add origin <private data URL> && git fetch origin && git reset --hard origin/main
unset GIT_DIR_ALIAS
It's not uncommon to initialize Git repositories to populated directories. E.g. that is how I clone my home directory skeleton on a new system:
git clone
https://codeberg.org/jarkko/skeletongit reset --hard origin/main
This is just extension to it. Home directories are great example use case also because then you could have separate Git repositories, if you want to isolate settings of a particular program but still have means to deploy them under the same root where they are cloned.