While the pirate flag idea may seem cool, it probably won't happen. Most pirate games were still released in specific regions, so they will retain that region code and the flag to go with it.
Awwww
You could still use the P for Pirate instead of U for Unconventional though.
There were some GBC games released without Nintendos liscense. I am pretty sure it was by the same company who makes gameshark. (Brain isn't functioning so don't remember who that is...,)