my guess is someone has tweaked growth requirements ,magical crops can be grown as agricraft crops, ive seen it several times . the fact nei is suggesting metal/gem blocks of a resource for the growing of magical crops is not a default thing.
That might be what's doing it. I considered that agricraft might be the culprit for the soil types but the entries for magical crops don't look like agricraft ones in NEI (they don't show the mutation source, probably because they can't be mutated like that). I wasn't sure either way though.