You are not reading carefully enough. The court ruled that the commerce clause does not give Congress the power to enact the individual mandate, that the argument that it does over reached. To the individual mandate itself it is more accurate to say that the commerce clause is irrelevant / does not apply, because it is a tax, based on the ruling.
To say that the mandate itself "over reaches" implies that the mandate itself is unconstitutional, somehow disallowed by the commerce clause, which is untrue.
Maybe you aren't used to thinking carefully about these sorts of differences, but the court sure did.