Twoshadows, It's believed by some that the Incuse might have originally been intended for either mint/proof sets, but the dies somehow got mixed up & some 'escaped'. Actual numbers of escapees is unknown. They're hunted down & captured wherever & whenever possible. Quite ofted held to ransom on Ebay!
The Proof coin theory sort of makes sense to me, as the 50¢ proofs had a coloured flag, so it's possible that was why the cross was incused. However, the proof coins actually have a slightly smaller flag , so if the incused was meant to be used for proofs, it didn't actually happen. I doubt that anyone knows the REAL story behind them, but I could be wrong.