Recounts can be done automatically for close elections, which means that the paper is authoritative.
A system is no more secure than its weakest link. Here we have two links where there used to be only one. So tamper with the paper ballots, force a recount and you win. Yeah this will cause a discrepancy with the electronic records but you said it yourself, the paper is authoritative so it does not matter.
In the 2008 Minnesota Senate election, one precinct's ballots were lost, and the authorities decided to go with the machine count for that precinct.
Yay! So you're saying attacking the other link works too: hack the machine count, lose the paper ballots.
It's hard to modify the contents of a sealed ballot box that has a chain of custody and bipartisan observers; most such fraud involves "losing" ballots, which is more difficult with the machine counts.
I guess that one difference of opinion we have is that I regard anything less than direct citizen oversight as useless. That includes 'chains of custody'. Even with supposedly bipartisan control. By the way bipartisan control makes it too easy for the two parties to make secret deals. I certainly hope there are in fact observers from at least three or four parties (and that car moving the ballot box around is going to get crowded).
Tampering with sealed boxes in a few precincts is going to cause serious discrepancies, which will trigger further investigation.
I also have very little faith in 'investigations'. We should all remember that the ones with the most to lose in an election are the incumbents who are also in the best position to steer the investigation away from embarassing finds. Furthermore we live in a world where investigations conclude that a satisfactory explanation for 4096 overvotes is "the spontaneous creation of a bit at the position 13 in the memory of the computer" and don't cause the election to be canceled.