I'm sorry, but the Classic Mode thing is not a discrepancy. Like, at all. That's just pure conjecture to begin with(there's no actual Grass types. In fact, PP not being there makes sense. It was, you know, never an idea for it. The lack of Olimar or Alph is the oddity, since that's actually based around specific Plants. Not a bonus DLC character, which again, is clear conjecture. They had confirmed base characters and ignored it, who fit just as well. The lack of any of them is equally strange, making it hardly a useful point of evidence in any way. That's ignoring actual context in this case. If PP was base, it would not inherently have been in that spot either. That's why it's purely conjecture). Nor is the spirit thing. There's really nothing special about that at all. Petey is not a regular Piranha Plant either. That's only slightly pointing to it, mayyyybe, but it's a stretch. Nipper Plant turning into Petey is strange on its own. But so is Toad turning into Captain Toad, despite them being entirely different people in the games. Spirits are extremely odd and don't follow accuracy to their games inherently. They just "are a neat concept" at times. Don't forget Sakurai didn't choose the spirits, his team did. They aren't going to be accurate about it all the time. They chose incorrect spirit images for things, including a fan image. Spirits are perhaps the worst argument for it. If PP was a removed spirit from the original list data-wise, then it'd actually point to it. And only slightly.
There's nothing "undeniable". Palutena's Guidance is unknown when it took place and is horrible evidence to begin with. Amiibo only mean something if you ignore any context of why not all are released at the same time. We damn well know some take more time than others. Again, the only actual questionable piece is the random missing data slot in the data at best.
The design philosophy doesn't work either. It also goes against being planned for base, since that would remove it from the initial project plan to put it on a new project plan. DLC is not the same "plan" as base game. I actually forgot about that key detail. If nobody was added or removed from the initial base game plan, that includes PP. He can't be "changed to DLC" with that in mind. It's far more likely he was always DLC and added to a new plan for it as early as March 2017, really. The reason for bonus is just like Mewtwo, who was not planned for base either, but to also promote buying the game early. Which actually makes sense for Sakurai, since it fits his entire philosophy more.
Just cause multiple coincidences exist don't mean they're anything but coincidences.
We won't know anything unless Sakurai says something, but trying to use flimsy evidence and pretend it's as clear as day won't make it so.