It actually does
Alt Characters don't have any moveset differences at all, not even in just their moves, but also hitboxes and animations and stuff like that. Daisy, Richter, and Dark Samus are pretty identical to their base fighter in moveset, but they have different animations that are too drastic for Alternate Costumes
On the other side, compared to Clones like Dr.Mario, Echoes are balanced solely against their parent fighter, and is a big reason why Echoes take little time compared to Unique fighters. Dr.Mario has alot of stat changes, Hitbox changes, and few move changes that drastically change how he plays compared to Mario, and as such needs to be balanced against the entire Cast. The Echoes, Including Ken, don't have that drastic of changes that requires balancing against the rest of the cast. It's very easy to make Lucina and Marth balanced to each other without affecting the balance as an example. Ken has move changes, but none of the New moves he has are so radically different from Ryu that it requires he be balanced against everyone else