Are envelopes generally involved? In the Antrim County dispute[1] it sounds like they use Image Cast Precinct (ICP) tabulators[2][3]. This[4] appears to be a video of one in use[5], and it doesn't seem to involve an envelope. If there's 100% mail-in voting then yes every ballot would have an envelope. But if there's any less than 100% then there will be less envelopes than ballots, so I'm not sure envelopes would be too useful for recounts.
[1] https://www.detroitnews.com/story/news/politics/2020/12/14/m...
[2] https://www.michigan.gov/documents/ag/SOS_Benson_Response_An...
[3] https://www.9and10news.com/content/uploads/2020/12/Antrim_Mi...
[4] https://www.youtube.com/watch?v=1t4l3eKRJv4
[5] https://verifiedvoting.org/election-system/dominion-imagecas...
My understanding is that in several places the envelopes in which the ballots were sent were allegedly prone to irregularities and the ballots have been extracted anyway and the envelopes disposed of, so recounts would by default take in account faulty/incomplete ballots if this actually happened. (no idea if the claim is true, however)