Are you talking about doing this for all future ballot boxes produced? If some customer wants this, just work out how much its going to cost, mark it up, and charge them for it. As for everyone else, the question in my mind is not so much "what would be the problems" as "why are we doing this"?
(1) Why do they need access to the yes/no buttons? To save the poll workers from having to unlock the flap to override ballots? Is that really such a big deal? Override should require poll worker intervention, and a key is the natural way to give them that authority.
(2) This one I really don't get. Tell me it is not voter receipts.