It seems as though the Geonim - although disparate and diverse in their opinions on many issues - seem to be rather united on the understanding of the Gemara on the subject of waiting after meat before dairy. According to the Halakhoth Gedholoth of Rav Shimon Qayara and the Halakhoth P'suqoth of Rav Ahai Gaon - and even Rasa"g, as quoted in a now lost portion of his sidur found in an anonymous commentator from Yemen on the Ri"f - one need only wash his hands (n'ttilath yadhayim/hidaha) and cleanse the palate (qinuah ha-pe) before eating dairy after eating meat. They do not require waiting unless one decided not to wash or cleanse their palate. I have found no Gaon who argues on this point.
My question is: If the Geonic tradition is clear on this point, why did some Rishonim require one to wait no matter what?