I've had 3 273 Commando's apart, a '65, '66 (out of my Formula S), and a '67, all three had the same bank specific, above the deck, pop-up pistons. I suspect when we see the flat tops appearing, in 273 cars, and keeping in mind how these cars may have been operated by their original owners, we may be seeing dealer warranty replacement short blocks that the dealer (or Chrysler) saved a buck on (or someone swapped the Commando/Charger short or long block out from under the intake and distributor). Since MOPAR didn't start matching numbers until years later, we only have date codes to know if a block or head is "correct" for the car. And of course it is also Possible (but I view it as less likely) that MOPAR ran short of the pop-up castings in production and used the flat tops to fill in the gap.
It would be interesting to know what the spec's on the cams are in the various flat-top blocks...