Summary: the current working directory of commands run through git aliases is wrong.
The easiest way to demonstrate this is to have a git alias like so:
This is clearly specified in the documentation as by design along with a workaround if needed.
Git Config Alias
Note that shell commands will be executed from the top-level directory of a repository, which may not necessarily be the current directory. GIT_PREFIX is set as returned by running git rev-parse --show-prefix from the original current directory