I'd noticed the topflashes weren't quite right but hadn't figured they were simply switched.
As you say, WillBorl, the holes do suggest these cases were made for the manual payout versions. Your picture reminds me that the payout cups were the wrong shape and, more significantly, too high compared to the standard auto pay machine. That makes me wonder - would there be room for the carousel payout mechanism? If not, were they using some sneaky electrickery for the payouts?