Before I offer my thoughts, this is a super valid argument. So what I am offering here is not so much a counter argument, but an alternative reading.
Having been reading about Mad Studies, which is about research and understanding the perception of people consider mad. I think a case can be made for a pro-Mad studies reading. Pinkie Pie performs in ways other read as insane crazy, or well mad. We Seen this various times. In this episode, all though Pinkie's perception and sense of knowledge do not immediatley make sense to others, they learn to value and respect her madness. It is not a tragic flaw, but a way of knowing and understanding the world. Twilight, who occupies the role of the sanist, a role founded on limited ideas of rationality and marginalizes folks considered mad, still needs to learn to respect Pinkie Pie like the other ponies in the episode. Throughout the episode, Twilight Sparkle either invalidates Pinkies claims, or tries to scientifically study Pinkie Pie to make sense out of Pinkie Pie from her own perspective. She has to learn that Pinkie Pie has her own way of knowing things, and even though she(Twilight) herself may not understand it, she can respect Pinkies Pie's perceptions and understandings as valid.