Correct me if I'm me wrong, but the charges aren't even for the documents he had and gave back the first time, they are specifically for the ones he held on to, right?
I was thinking about this some more, and granted none of what I'm saying is based off of any legal knowledge, so take it with whatever grains of salt. If low-level random guy A gets caught with a document or two, there's a question of why he ever had that document in the first place, if not for nefarious reasons, since the document had nothing to do with him. If a former high level member of an administration ends up with some documents, there's a good chance those documents relate to them in some way, given all of the things they came into contact with a POTUS or VP or something high level. That's what at the end of administrations they have a big big review process to go through all of the documents that officials have on them that they may want to take with them to use in libraries or memoirs or other legit reasons. It is not inconceivable that given these hundreds of thousands of documents that some may work there way through the review process that should not have; the reviewers are only human themselves. So if you have it on record that the people in the administration went through the correct review process (which you do for every administration except the last; if the last did do it, it certainly didn't make the level of news it usually does), I'm not going to be surprised if some that should have been removed make it into their possession given the pure volume. And if/when they do make it into their possession, then it comes down to how they react and cooperate. Biden and even Pence immediately did everything they could to cooperate; that's why no one is going after them. Trump hid and obstructed in an almost comical fashion; that's why he is hopefully getting the book thrown at him.
But my above point is, there's a reason why "former POTUS/VP ending up with 20 documents" != "corporal shmuck ending up with 1 document".