Considering Spirits are just one image, and every Fighter Spirit is different from others, there's no reason to believe they alone would suddenly disconfirm someone.
AT's may. But things like "in someone's Final Smash/Victory Screens" have proven to be meaningless. Chrom pretty much removes any possibility it would've mattered. If it did, he wouldn't be among the Final Smash and Victory Screen still. That was intentional to not worry about it. To drive it further home, Mario is in PP's Victory Screen.
That really leaves Bosses, AT's, stage hazards/elements and active in someone's moveset(ala Toad). You can have bosses play and look differently at times(Ganon, for instance), AT's can be turned off while the playable character is in the current match, stage elements can be removed, but you can't just remove moveset stuff like that. You also can't remove certain kinds of stage elements/hazards. For instance, Pauline is too important to the stage's design. On the other hand, you could easily remove Captain Toad from it. It's not black and white for how stages can work, really. Toad is directly disconfirmed, though. You'd have to give both Peach and Daisy something completely different in order for Toad to be playable. This is very difficult to remove in comparison to most of the rest. For the Pauline point, she's like DK in the 75m stage. It's a key part of the stage. Whereas you could simply not have Ridley or The Ultimate Chimera show up without making the stage beyond different. It's not as simple as turning off hazards, but whether you could easily remove the stage elements without making the stage impossible to use. If you need to force a stage as Alpha or Omega to have a character playable to not confuse players, then they're clearly a key element. Another good example of something not hard to remove is Tingle from Great Bay. The reason is you don't need that hazard that much, but you could also replace it easily without another MM character(even Deku Link) and nothing would change. It's barely a hazard.