1. As you said, Cloud of Darkness is assumed to have been blasted by the Warriors of Darkness before the fight, a la Crystal vs. Zeromus, Star Dragon Sword vs. Neclord, Psychowand vs. Zio, etc. Pretty strong precedent here and the alternative is she's just invincible, which is obviously unrankable.
2. Yeah, you have a pretty good summary of why FF3 individual PCs get a big ol' DNR.
3. The helper PCs are even less rankable, though - they have attacks, yes, but no HP, and generally do not function is normal characters in battle would. It's a situation more similar to that of XG Margie, who is more important plotwise than any FF3 helper, and from a bigger game, and in all versions of said game, and is still not ranked and considered unrankable by most. Heck, we didn't even rank Charmles, who is like the FF3 helpers except he actually has a win/loss condition from in-game.