Have done a bit of looking around and the proof 50c coin was not stamped at all with a flag design, it was painted on the coin.
No Incused coins have been found in mint sets that I know of
I think this is a case of one die was made, they minted the approx 200,000 circulation coins from it, and for some reason didn't continue with the same design when it came time to relace the die. It may have been as simple as the die dint actually produce the number of cons it was designed for and failed early, thus they had to go back to the drawing board and slightly change the design.

