There are reports some of the ballots counted were nothing more than photocopies in Michigan, If these ballots were disappeared after the election then they won’t be there for a recount but if they are still there then yes you would be able to detect fraud ballots even outside their envelopes.
What you need is an audit of a statistical random sample of the envelopes separate from the ballots with a detailed canvass which would be separate from the ballots being recounted. Part of the audit is to count all the envelopes, there were reports that naked ballots were fed through the machine, these are ballots without envelopes, these would show up in this audit as well.
Depending on what is found, the up to the entire county could be wiped out.
You make an interesting point that I hadn’t thought of. It’s easy to tell whether something has been printed or copied. Any copied ballots should be thrown out — but not before the votes on it are noted, so that a trend (like how many voted Dem and how many only voted Biden) can be discovered.