Something has changed though and that's timing. Assuming that the Fighters Pass was chosen alongside them choosing Spirits that would likely mean that they had no plans for those characters currently at the time of choosing the FP specifically the post-FP DLC could've been selected after the FP DLC in which case they could've changed their mind about a select few characters in-between the two projects.
Maybe I'm wrong but the timing leads me to believe in the possibility of choosing some spirit characters to upgrade.
That’s my point though. If the amount of “popularity” was there prior to the Fighter Pass, and they still weren’t chosen, why would that same level of “popularity” get them in now if it didn’t get them in before?
Again, the idea that the character would get upgraded because they’re popular seems to ignore the fact that despite their popularity, they still crossover over, just not as playable in the first place.
I see spirits having a good chance being upgraded post-FP if they're from games not represented as ATs or fighters yet (or Geno because Smash Bubble). Characters like Isaac, Shantae, and Custom Robo would bring new worlds not yet fully represented in Smash Bros, which falls in line with Sakurai's mission statement.
That comes down to Sakurai considering Spirits as “part of the crossover”, which, I’d argue he does. At least he hinted at it in a SG translation. He effectively mentions that, “when you consider Spirits in the game, it truly is a massive crossover!”
Still, with games “not fully represented” that still doesn’t explain why he would/should pick characters already in Smash one way or another when he could continue to pick content that is not already in.
In terms of Nintendo, Astral Chain comes to mind. With 3rd party companies, there are several.
I’m very likely not going to be convinced that spirits will be upgraded. But depending on the character, I would happily be wrong. Isaac or Rex for example would made me absolutely satisfied.