I'd wondered that - but it doesn't seem as insurmountable.
I don't think that they can just cut the Spirit - now that each spirit has a battle and effects, you can't toss it. But what could be done is replacing it, so you still keep the Spirit, it just has a different name/picture. They don't have any descriptions, so that'd work. My big example is Tails - the battle is against a Fox (yellow jacket) with a Jetpack on Windy Hill with a Knuckles assist. The Spirit you get is a three-star support that boost uSpecial. If Tails made it to playable, they could just swap out the .png for the art for something else (like Tails' biplane, the Tornado), and the battle would still make sense. (More actually, since the fact that the Tails battle didn't involve Fox with a Super Leaf is BS)
Of course, this may be overthinking it, and they'll just leave it like with all of the Chrom stuff...