Just remember, they had Dr. Mario and Mario in, who are supposedly the same person. In a series that has no real canon to speak of. They also share the same symbol as well. Also keep in mind Metal Mario was a fully separate character in 64 as well.
I don't think Sakurai cares at all if the same person or "character"(that is, two versions of Toon Link, which is confirmed) appear in some way. So really, I don't see how this affects Ridley's chances at all. Notably, they have two main Ridley designs, regular and Meta. They could use the opposite one, assuming one appears in the Pyrosphere in the first place.