When you run load_all() on your package, the devtools:::shim_system.file function gets inserted into your package's imports environment, with the name system.file. So if any functions in your package call system.file(), they'll see the shimmed version (when your package is loaded with load_all()).
It's not exported because there's not a reason for most users to call that function directly -- the original intended purpose of the function was only to be used as a shim as described above. The fact that devtools::system.file was exported in the past was because we had not yet thought of the current (cleaner) way of adding shims.