Just functionally, it seems reasonable that something happened before that bad feeling to trigger it, e.g. "trying to fit this with already known things, and finding it doesn't".
Every website you visit has the payload delivered over the network before any JS is parsed. It has to, there's no other way. Same with intuition followed by rational thought
I guess if you define all rapid cognition as Intuition and all slower conscious cognition as Rational Thought, you're right by definition, but while that might provide a happy feeling, it might not give you any useful insights upon deeper inspection.
For instance, it doesn't support or disprove the "less emotion is bad for thought" idea