When you vote in person, the trust-level of the result is high.   I fill out my ballot, I walk to a machine with a poll worker and I insert it in and my vote is cast.

But with mail-in votes, especially ones where the ballot applications are mailed out, you have a bunch of vulnerable points in the process:

1. You have the possibility of harvesting the applications.  Picture an operative going to a college dorm or a high density housing complex and going door to door to gather those applications and sending them in.   This part isn't particularly problematic because it's just the application.
2. The follow-up, called ballot-harvesting, is a much bigger problem.  You have operatives arriving and ensuring that the people vote "correctly" and then gather up the ballots and send them in.  Anonymous voting is extremely important for reasons that have been widely discussed elsewhere.  Ballot harvesting is very difficult to prevent in this system.
3. In both 1 and 2, you are relying on the application and the ballot to, in general, make it through the mail system.  These ballots/applications can be easily lost.  Which way different neighborhoods tend to vote is not an mystery.
4. You also have the issue with people who shouldn't be voting voting.  This is the "no voter ID" issue on steroids.  Whether it be adults voting in place of their parents in nursing homes or even people who just shouldn't have received an application because they died or moved and having an operative take care of the rest is a problem.

Now, in none of these examples can this make up for a massive lead.  But it can probably generate a 1% delta in a given state. 

This is why, for the integrity of our system, voting should be done in person.