DonnyKD, as you correctly recall, SMB2: USA did begin as a separate game. However, Yume Kojo: Doki Doki Panic was not planned for export, and was written off early on as a throwaway licensed game for a TV channel.
Worldwide, it was transformed into a completely separate game. Yes, they shared sprites, music, and a game engine, but SMB2: USA had its own characters, power-ups, story, bosses, and rules that made it distinct from YK: DDP. That alone, in my opinion, is enough to have SMB2: USA as a real Mario game.