While it's pretty clear with hindsight that base game spirits were a deconfirmation for Fighter's Pass 1, I don't think the same applies going into season 2.
For the base game, the spirits list was picked by a separate team, with Sakurai reviewing their options and adding/removing characters for a variety of reasons. As such, I think one of Sakurai's criterion during this process was "Are there any spirits who overlapped with a fighter?". Additionally, given that the first fighter's pass was finalized late into the development of the base game, it was pretty likely this applied to the DLC characters too. Combine this with the fact that Sakurai assumed that the fighter's pass would be the only DLC content, he didn't have to worry about having overlap between the fighters and spirits in the future, as he knew (what he assumed would be) Ultimate's final roster.
However, the Fighter's Pass isn't the only piece of DLC coming, we have six more characters in the oven as we speak. As such, there may be some characters who slip through the cracks and have both a standard spirit and a DLC spot. Sakurai wouldn't have vetted these characters out as he believed that the base roster and fighter's pass would be all there was. Likewise, I don't think Sakurai is going to block out a potentially interesting option solely on the grounds they had been given a spirit when he assumed there was no way for them to get in the game.
The only potential exceptions to this are the spirits that came through downloadable updates. If they were decided after Fighter's Pass 2 was finalized, then I think those spirits are effectively deconfirmed. If they were decided before Fighter's Pass 2 was finalized, then they're probably alright, as there would be no need for Sakurai to vet them out.