I don't think it's as clear as you say that this is just a common regional version. As mentioned, the unaltered base games were also released in these regions. So I don't think your analogy to Contra or Shatterhand or the others is as applicable here.
Also, I have to refute that the only changes were a simple sprite swap for the main character. In Sapo vs the Swamp Invaders, multiple character sprites are changed, not just the main, and there's even new weapons added (Sapo Xule's stinky shoes). In Sapo SOS Polluted Lagoon, enemy sprites and powerup boosters have changed in addition to background palette changes and the player's ship sprite.
But mostly I'm really concerned for the implications this has on romhacks since those are the majority of adds that I make to the database. I can think of at least a dozen romhacks for just Sonic 1 and 2, not to mention many more for popular mario series games where the only change to the game is that the main character that you play as has changed, and I can't conceive of anyone who wants a dozen different romhacks jumbled together.