The Japanese version has very barebones copyright details.
The European release changes the background colour, expands the copyright jargon, gets a brand new logo, and adds a trademark symbol.
The American version keeps the Japanese title screen but holds onto the European version's expanded copyright and TM symbol.
The white church in the intro and ending has a cross on top of it, which was removed from the English versions to comply with Nintendo's regulations regarding depiction of religion.
As was the standard for the era, vowels in the password screen were replaced with numbers (Japanese password IHINHLFC becomes B8BH8F63 in the English release, for instance). Despite the changed symbols, the passwords are technically the same in all versions; Japan's A and I become the English version's 1 and B, for instance.
The title on the super secret sound test room was changed between all versions - for the new title in the European release, and to adjust parsing in the American revision.
Graphics for Kondoria from the PC Engine game exist in the ROM, but the enemy appears nowhere in the game. Although a regular enemy in the previous NES instalment, the PC Engine version only utilised it as a battle mode obstacle.
Due to the fact the game is one of the rare NES titles to have graphic compression, I can't find out if there's anything else unused.