It turns out that when deploying using file paths the scope remains the client scope. This seems to be by design, therefore, I had to search for another publishing option.
I now use WebGitNet (github.com/otac0n/WebGitNet) for pushing, which enables me to post over http(s) and doing this, it also operates in the server's scope. Currently, I am also pulling using the same mechanism, but I don't have to - for speed I could also choose file system access for pulling...