As long as the chain of custody is maintained, a recount of a paper election is repeatable and can be verified with physical artifacts (ballots). Unlike a paper election, there is no tangible evidence that records have been maintained securely. Additionally, even if a box of ballots is stored insecurely or somehow goes missing, in most cases it isn’t a showstopper as the margin of votes is still comfortable enough to have a clear winner.
Except in very close elections, traditional paper elections are almost impossible to manipulate successfully if the custody and counting process includes representatives from opposing political parties. (Week long counting periods that accept a million delayed votes are another story, but that is a process issue and a deliberate decision to weaken electoral integrity.)