...it was never NARA's document to begin with. This section of the opinion is referring to an "agency", not NARA.

The issue discussed refers to a document BELONGING TO AN AGENCY beneath the president, but Trump's (or any president's) copies of such records did not belong to any agencies; they belonged to him. If he is given a copy of Document X, then that document belongs to the president, not the agency. First off, it's a copy, so the agency itself has not lost possession of anything -- there is nothing to return, as the agency already has the document in question. (And don't come back with "oh, what if it was top secret blah, blah, blah". Doesn't matter -- a president, as head of the executive branch, has the right to possess ANY document.)

Second, it is HIS copy -- his property. He then has sole discretion as to whether to classify it as a presidential or personal record. If a president takes documents home with him, then they are presumptively personal by definition (and this is aside from the fact that a former president has YEARS to determine after leaving office how to make such decisions, which is why there was a back and forth between Trump's camp and the NARA to begin with occurring years after he left office).