I've said it before, but I'm still not convinced that Alph was meant to be clone at one point instead of just always having been planned as a model swap. The phrase used in the balance checklist that Source Gaming translated (モデル替え/"model swap") could potentially apply to either a separate clone fighter or just a model swap for the same fighter. The fact that the term for normal palette swaps (カラーバリエーション/"color variation") wasn't used for Alph makes sense in either situation, because Alph isn't a normal palette swap, he's a complete model swap. Also, on the translated balance checklist, Alph is only mentioned for the modeling team, but if there were plans for him to be a separate clone fighter then he'd require work from the animation and game design teams as well for his slight differences, so why is there no mention of that?
It'd be nice to see the original Japanese balance checklist, but Source Gaming haven't provided it, and I haven't been able to find it elsewhere either. Knowing whether or not Sakurai has ever referred to other literal model swaps like the Koopalings and such as "model swaps" instead of "color variations" would also help clarify the situation, but I haven't seen any examples of Sakurai speaking about those with specific terminology, unfortunately.
At the very least, new articles reporting on Bowser Jr's official unveiling used the term "color variations" for the Koopalings.
https://www.inside-games.jp/article/2014/10/24/81836.html
Same goes to fan wikis. I can't find anything directly from Nintendo or Sakurai himself, but the usage seems very spread for the Japanese side.