Olimar and Alph have barely any differences, though. Toad and Captain Toad play extremely differently. Hell, they're from essentially different genre of gamepaly.
Dark Samus is also a special example of an Echo who wouldn't have gotten in otherwise. Unlike Captain Toad, Dark Samus also can perform very similar skills and it's even an in-universe reason. She's using Samus' old suit. This doesn't apply to Toad and Captain Toad as they're designed quite differently. And we're not talking about an Echo situation either way(which definitely wouldn't work either, as Captain Toad really doesn't use Toad's gameplay anyway. Not unlike part of why Isabelle isn't an Echo, though bodyshape was also a major role and a rule to why one can't be an Echo). Daisy is also a very badly done one and should've had a minor difference like Richter or Dark Samus do. Not a "one that exists, but is barely noticeable".
As I said, the analogies simply don't work. The only thing they have in common is bodyshapes, but that's it. That doesn't mean they can't work, but the reasonings don't really hold up with the analogies.
The main thing anyway was "why are they separated?" And that's because they're different characters. The fact they're much more highly different than what would expect also helps too. That said, Captain Toad works fine as an alt anyway because the rest of the stuff would have no effect on gameplay. It's as minor as Meta Ridley's changes. On the other hand, if that's treated as "too much bulk for the model", then it wouldn't happen. Technically speaking, the changes with the backpack are a bit bigger than Meta Ridley's model differences, but it doesn't feel that big of a deal. So it could work. Sure, it would make Captain Toad look fairly OOC(far more than Dark Samus who is remotely believable with Samus' skills), but as said above by Fogbadge; "I'll take what I can get."
