Regarding the whole "spirit names and pictures" thing... I don't even think it's much of a roadblock honestly. As I said in prior post, Sakurai and Nintendo will do what they want if they really want to do it (barring limitations set by third parties). Also, everything base game was set how it is now before any of the packaged DLC additions were officially sorted out. Piranha Plant stands on it's own and was clearly in development before the game was carted and shipped.
This all said, if you still have hangups about potential DLC characters having spirits already and feel that spirit names/pictures/events are something of a deconfirm because Sakurai and Nintendo wouldn't want that conflict, here's some interesting things to consider...
1. They didn't change trophy names for Lucas or Mewtwo in Smash 4, so there's evidence that they don't even care about this naming convention conflict.
2. Theoretically, it wouldn't be that hard to change the names or even pictures if they really wanted to.
3. For Rex and Pyra/Mythra specifically, it's largely assumed (and if Sakurai is gonna be true to source material) that these characters would be "one playable character". So technically, the "playable character" is a "team" like Ice Climbers. So far the Rex, Pyra, and Mythra spirits have been only one part of that potential "playable character". Would be like seeing a Nana spirit and saying Ice Climbers are deconfirmed. Basically, the potential playable fighter spirit could be these same pieces of art but Rex and Pyra/Mythra together and their name wouldn't just be "Rex" or "Pyra"... it would be "Rex and Pyra" or "Rex and Aegis".
4. If for some reason they add an XC2 character but it's not a team but rather Rex on his own or even Mythra or Pyra on their own.. the first and second points still apply, with them changing perhaps the pictures and names only as much as they feel they should.
I think these points pretty much put to rest the spirits conflict... at least in my own mind. But at the same time I acknowledge that while everything I said above is true or likely to be true, this in no way confirms that even any current spirit will become a playable character. I just think if a spirit doesn't become a playable character, it's far more likely for reasons other than "we didn't want to rename a png". Basically, if Rex and/or Pyra/Mythra don't make it, it wont be because they were spirits. That doesn't make sense when considering the timeline for the DLC to be sorted out, and it sets an unrealistic limit on the game as if Sakurai was supposing already what they'd never do even if Nintendo asked.
...
One thing I do want to wonder aloud about tho is... how would their amiibo work? Again, assuming a team playable character. ICs are on one stand... but I don't know what PT is doing in terms of amiibos. Is each Pokemon getting it's own stand to match with the solo Charizard? Rex and "Aegis" would be a weird in-between where I could see Rex and Pyra cramming on a single amiibo platform, but Rex, Pyra AND Mythra? I think knowing what PT is doing would be very enlightening.
Otherwise, our only reference for how they might do this is to look at the two Clouds or the two Bayos. Maybe Rex has an amiibo where Pyra is with him and a different one where it's Mythra. Tho in the Cloud and Bayo case, they're representing different costumes, not different "modes" of a character. Of course, it could just be Rex and they forget either Pyra or Mythra on the amiibo. Or maybe the playable character can't swap blades for some reason and then the amiibo choices would be simplified. Or maybe the playable character is literally Rex with no blade for some even weirder reason and then that "Rex only" amiibo would obviously make sense. Again, I wonder what they'll do for PT. They have to be, or have been, chosen for DLC before it's even a concern however.