Use rel filepath in auto generated kustomization

This works around another bug on Windows platforms that would cause the
kustomize-controller to choke on the kustomization.yaml generated by the
bootstrap command due to the filepath being in a Windows format.

By using `filepath.Rel`, the output is _just_ the filename for files
relative to the bootstrap path, which is at the moment sufficient to
make it work.

Signed-off-by: Hidde Beydals <hello@hidde.co>