Safe Harbor in these types of cases -- which will keep coming -- will continue to be decided at the appellate level, and the decisions will depend on the composition of the panel of judges and the venue.
Another scenario could be MNTA M-copax gets approved, another company then gets it approved via the same way Ampha got theirs, MNTA sues for infringement, gets a different panel at the CAFC and wins that CAFC case. Wacky indeed!