But, invalidating this patent on 101 grounds versus 103 grounds is not the same. Subject matter eligibility is something that can be ruled on in a motion to dismiss, In re Bilski, 545 F.3d 943, 951 (Fed. Cir. 2008), while obviousness will generally need to wait after claim construction. It should be possible to knock out patents that claim a fundamental practice in any field as early as possible.
You can make other distinctions between "a fundamental practice" and "prior art," too. In the field of cooking, do we have to point out prior art for making a roux, or do we just accept that someone, perhaps many someones independently, did it sometime long ago, but it's so established now that it might as well be a fundamental law of the field?
Over time, the Supreme Court has been beefing up 101 as a bar to patent eligibility. Is the interpretation in CLS v. Alice the one that's most faithful to the text of the statute? Probably not. But interpretation in the name of controlling the flow of litigation in lower federal courts is one of the key roles of the Supreme Court.