My understanding is it's like, the only classes that are supposed to exist are the seven main ones. That's why they're the only Grands (ORT's hacking notwithstanding). Ruler and Avenger were created by the Einzberns, Alter Ego and Moon Cancer were created by BB, etc. So human history is rejecting Chaldea because its use of Extra classes is unnatural.
Why this is only a problem NOW and not earlier, I'm not sure.
Maybe? Rulers and Avengers are (originally) supposed to be Grail War specific, with Rulers acting as impartial Grail-related arbitrating, and Avengers being... well, Angra Mainyu. And the Chaldean only specified Alter-Ego, not MoonCancer, which is interesting. Though with the vague EXTRAverse references, I feel as if MoonCancer will be part of the trial regardless.
However, the Chaldean also implies that those three classes have some use to the Human Order, meaning that Ruler and Avenger aren't just Grail War aberrations, but also have a broader use in protecting the Human Order. And the Counter Force has already made use of the Alter Ego class (Okita Alter) for their own purposes before. So those three classes are SUPPOSED to exist, but something (as in most likely the Chaldean FATE system) caused them to operate in purposes outside their original intention- and as Chaldea represents the last of humanity, if they restored humanity with an 'imperfect' viewpoint of what those classes meant, it may cause damage to the Counter Force, Human Order, or whatever. Kind of like using a 'sequence break' in a videogame, and potentially breaking some of the 'code' later on in the process.
So this will probably be going back to grassroots for the classes. Our 'Ruler' will be more like Jeanne, our Avenger more like Angra, and our Alter-Ego... well, who knows. I suppose an entity akin to Okita Alter.
The strangeness also comes from the fact that, if we left out Summer Servants, none of those classes really have a huge 'misunderstanding' outside of maybe Alter-Ego.
So I think it weirdly comes down to why THOSE classes specifically, as Chaldea made use of classes such as Pretender or Foreigner that would ultimately be considered as more of a threat to the Human Order.
If the Chaldean said 'you summoned Foreigners and Pretenders, which are canonically against the World in some fashion', then I think it'd feel less strange. Especially after Chaldea literally has a part of ORT itself manifest via Kukulkan.
