Accepting defendants’ contrary arguments would transform section 271(e)(1) into a royalty-free, open-ended statutory license for the use of patented inventions in commercial drug manufacturing. That result cannot plausibly be attributed to congressional design.
FWIW I would suggest that the MNTA patent rulings are just a symptom of a long history in patent law (and society as a whole) that raw ideas are not 'ownable', no matter how temporarily (this has a long basis in patent law, although it has had to change, slowly, as innovation moved further and further from pure physical objects). And, having read many legal opinions, it is pretty clear that unless the law is completely and absolutely unambiguous many of those judges will find some reason to invalidate. I refer to it as IP Communism.