If you want the file to appear instead of the link, you should probably use the ln command to create a hard-link instead of a sym-link (ln -s).
Making a hard-link, you can make the same file to appear under two different directories, so changing it via any of the links will reflect changes via both links, and the file will live in both directories, so it will be tracked by git.
I hope Windows’ mklink /j command in Bukov’s answer does this, but I really don’t know at all.