PBA: Because, once again, you are misrepresenting his opinion. He does not say that only his rationalists are right and that the others are wrong. He accepts the mystical Shittos as a valid and important part of our Mesorah. He just doesn’t think that they are Pashut P’shat. There is a huge difference there. You see it when you learn any Sugya. Some Rishonim have Dachuk Shittos. We don’t treat them with any less respect or dismiss them. But when discussing the Sugya we have to point out the Kashyas and why we think they are Kashyas. And sometimes we are forced to say that we cannot, in good faith, figure out how this Rishon read the Gemaras. It’s the same thing here.
Whether or not it was accepted for the past millennium is interesting because no one really (outside of the Rishonim who couldn’t create a consensus because most discussed these issues independently and didn’t build off each other) bothered to discuss this issue directly until the whole Slifkin saga exploded. (Well, the Chazon Ish did, but that doesn’t create anything near a consensus either).
To your first paragraph, you know that you are just being glib. You really find it entirely untenable to believe that Slifkin’s super-rationalism isn’t Kefira. In general, the onus of proof lies solely on the one that wants to call something Kefira. As long as Slifkin has a strong list of Rishonim in his corner and no massive Haskama throughout the generations against it, I really don’t see how it can be called Kefira. If you want to say what he says is Mach’chis Magideha, you need an incredibly strong Ra’aya for it. I don’t think such a Ra’aya exists. He is wrong and misguided, certainly. But I can’t see how you can call him a Kofer. To do so would be to call the Rishonim he’s agreeing with Kofrim as well. No one alive today has that Koach. It would have taken an immediate M’cha’ah from contemporaries as well as hundreds of years of rejection of these Shittos. That’s how we invalidate Shittos in the Rishonim. That didn’t happen here. I don’t know why people are trying. People should actually deal with Slifkin’s sources and explain why we don’t hold like them. Pretending they don’t exist only exacerbates the problem.