The Tur quotes Rav Natrunai Gaon’s responsa, so it is not just Rishonim mentioning a Minhag of the Geonim; it is in writing from the Geonim. Rashi too was quoting what he saw from the Geonim.
Now, this actually is explaining what the Gemara means by Purpisa. He says that he saw from the Geonim that they did Zeh Tachas Zeh with plants. This should serve as an example of a Minhag that the Amoraim had but was not explicitly recorded. They referenced to it as an example of a question in Hilchos Shabbos, by chance. So perhaps the question itself, what is the Mekor, is refuted by this very topic.