Chrom also wasn't in the same situation overall. He was a minor cutscene move and some victory screens. Final Smashes aren't nearly as common as a Neutral B move and throws, so the comparison doesn't really work all that well. He also was outright considered, and then later became an easy Echo(and even then, all they did was not change Robin as much because it's new animations for something that already works fine).
Toad from the start was a move that was easy to replace as is. In Ultimate, now he's a far more heavy part of the moveset. Unless Toad was considered and turned down as soon as Melee(something we don't know), they couldn't be in the same situation. Being a popular pick doesn't mean the character was outright considered. Maybe that's why he was made into a move as well, because they couldn't think of any abilities at the time.
He is missing, but he's not in a Chrom situation in itself. ...Unless you can think of someone Toad can be an easy Echo of, anyway. That's kind of the key thing that got Chrom in, ease of creation. Liberties were taken for animations and even a new Up B, but they had a clear moveset to work wtih.