You could say that while Zelda/Sheik and Samus/Zero Suit Samus are separate toys, they aren't separate characters in the imagination world, which could be used as justification as to why they share a slot on the CSS too.
Although going with the imagination world idea does mean you can kinda just say "it's like this because I said so" so perhaps that's not the best way to handle it, but it's also a crossover title which generally need a healthy dose of that anyway so pluses and minuses I guess.
Honestly, the worst part is that when they did that, which is they count as separate Toys, it meant in All-Star and Classic, to get each Trophy, you had to beat it as the specific character(Samus, Zero Suit Samus, Zelda, Sheik, Squirtle, Ivysaur, Charizard). This made it a massive pain for no reason. Melee didn't have this issue. I don't remember how Ultimate handled the two Transformation characters, though. 4 never had the issue, though it was still a long process either way. Pokemon Trainer and regular Samus suffered the most. It was very easy to get knocked out of one specific Pokemon to get the final one, and you couldn't easily return to regular Samus state(which while this showed how they intended Zero Suit Samus to almost play like a separate being, with clearly not being tied to Samus even then more than a Final Smash gimmick, it was still tedious to deal with the consequences of that decision).
Like, it's perfectly fine for a story, but Classic Mode is not the story mode at this point. You can shortcut and get all appropriate "toys" from beating it. It's fine to have it separate for something like All-Star and Adventure Mode(the latter being Melee-like for this example), but only in the sense of "you get the Classic Mode toys, and then you get the Adventure Mode toys, and then you get the All-Star Mode toys. You don't need to do it freaking again as the other transformation). Ultimate's Adventure Spirit stuff never dealt with this issue, thankfully. It was nice and clear.
