No, 9 times out of 10 they aren't talking about Captain Toad. Some think they are the same character, but that's a US only thing due to a bad strategy guide, so it's not their fault they were misinformed. Doesn't change that two entirely different characters are being supported.
Oh, and Pig Ganon is absolutely wanted because he's a different version from Ganondorf too. That's one of the biggest reasons he has support, due to unique abilities. Not just being iconic too. He's actually far more spellcaster-like than Ganondorf ever was(who actually focuses on being more physical in games now, though that was effectively planned since after OOT, and even his artwork shows him being physical). Being iconic isn't enough alone. People do care about movesets too, since that's what helps them support others. ...And why do you think ZSS is liked? Exactly. Movesets. These are a huge reason for character support. This is why there's support topics for a BOTW Zelda, Link's Awakening Link, etc. They do matter a lot, honestly.
I'm not saying they aren't mistakeningly supported like they're one character, but at the end of the day they aren't, and that matters too for Sakurai. He doesn't group together characters as alts unless they actually can share the same abilities, and well... these two just plain don't. Even Bowser Jr. is lucky to have those alts, because of the Clown Car specifically. That's the entire moveset, and it only has like one Bowser Jr. specific move, being the Final Smash. Pikmin and Alph is an alt cause he literally has no unique abilities from Olimar as is. He was an easy one with a slight adjustment of the model, and since the Pikmin are a core part, there's even less reason for a split right now(especially as it was only during Smash 4 Pikmin had enough relevance to justify an echo/clone. Ultimate... it was pretty much dead, so. The other Echoes made more sense due to the series they're from or other special situations like Simon/Richter specifically borrowing from each other).
I get what you're saying, but you're oversimplifying the support too.