Whats your version, because my version, even with your pk4 file, return the same legality check.
But... here a some strange things about this:
If I open a extracted pk4 file of my Cherrim and your alone (without a dsv file open before) the legality checker returns a Legal
But if I open the same pk4 files with a previos gen IV dsv file open in PkHeX, the local warning from Legality Checker happens