There's a potential implication that the president wasn't the one making the decisions and they were political favors doled out by unnamed and unaccountable staff. If the president felt strongly about that perception he could've signed them himself. But he seemingly didn't.
The controversy with Biden is that the autopen was allegedly used without the President's knowledge or directive. Nobody has a problem with POTUS's signature getting on a piece of paper without his hand actually holding the pen; that's not the point here.
"Allegedly" is the key word here. Alleged by people who allege a whole lot of untrue things and don't seem to have any evidence for this particular thing.
There's a conspiracy theory that Biden wasn't competent enough to sign stuff, at least for some period at the end of his term, with the implication being that none of those presidential acts are valid. Anybody who believes this is mired in an impenetrable misinformation bubble and should be dismissed out of hand.