Agree. In fact in MA and NC where I have voted by this mechanism, in practice it appears to work more or less as you say. I mark my paper ballot, then in MA place it in a cover sheet for privacy, hand it to the election official, then watch her feed it into the machine reader, which reads it and stores the hardcopy. In NC I mark the ballot, then feed it into the reader myself. In both cases I know that physical ballot is in there, in a stack in the same order in which my vote was tallied electronically.
The Diebold-type technology ought to be outlawed at the federal level, if that is legally possible.