That's a fair summary of the finding (and I would contend, the major issue in this case).

The counter-argument that might lead one to disagree with this decision is that the Patent Office reports to the President, so it is subject to the political motives of that branch.

For example, let's say, a major democratic donor receives a software patent on a novel ML algorithm useful for predicting voting behavior. Under inter partes review, the President (or his subordinates) could invalidate that person's patent if challenged regardless of the evidence. If inter partes review were found unconstitutional, they would need to convince a jury that the algorithm was, in fact, inappropriately granted.