We have never gotten an alt character skin, therefore, we have no idea how it would be handled.
If they are separate characters, why would they not have different pages (just as sheik and zelda) yet one slot on the select screen?
Maybe the word 'skin' is too much of a trigger word, so instead I suggest character alt, a la the stated Kuma/Panda or Roger/Alex from Tekken.
I'm not saying she is not considered a newcomer, but there is no evidence to state that pure clones who fight identically are not just character alts. In fact, we have reason to believe otherwise.
-character customization
-confirmed skins in addition to palette swaps
-no confirmed old clones (except Toon Link, who has remarkably different hit boxes)
-rather unkind treatment of Chrom (which, I admit likely rules him out, but still there are elements that are questionable if we look at him as an unlockable alt skin for Ike).
Even Chrom's reveal leads me to think he could be an alt skin for Ike, and that we have three FE character playstyles (Marth, Ike, Robin), and then Fan service in Lucina and Chrom being playable as alt characters with an identical final smash.
I'm not a Gematsu guy, in fact I was in huge protestation of it for long periods of time. Maybe I'm just a hipster at heart, but perhaps there is some credence to it. Perhaps all four swordsman (Lucina, Marth, Chrom, Ike) were in fact all planned to be in, and Gematsu made the reveal order a bit askew (swiching Ike to be revealed earlier to shock people, then Lucina now instead of Chrom-- I mean, if all four can be playable, in terms of game context it would make sense for Lucina to be unlocked).
I got into a bit of a rant there based on todays reveal- but the first half remains accurate. We have not seen alt characters handled in smash; the closest we have seen are multi-character fighters, which do have separate pages, and there is thusly no reason to think that alt characters would not then be labled newcomers. Sakurai always honors his characters.