Here are two possibilities for the source of the minhag.
The Yerushalmi makes the same statement that we have in the Bavli, that dough made from rice and water undergo a sirchon, not chameitz. Then it continues (Pesachim 2:4, vilna 17a):
רבי יוחנן בן נורי אמר קרמית חייבת בחלה שהיא באה לידי מצה וחמץ ורבנין אמרי אינה באה לידי מצה וחמץ ויבדקנה על עיקר בדיקתה הן חולקין רבי יוחנן בן נורי אמר בדקו’ ומצאו אותה שהיא באה לידי מצה וחמץ ורבנין אמרין בדקוה ולא מצאו אותה שהיא באה לידי מצה וחמץ.
Rabbi Yochanan ben Nuri said: Qarmis (millet or something similar) requires [giving] challah [from the dough to a kohein] because it can become chameitz or matzah.
And the Rabbis say it doesn’t because it can not become chameitz or matzah.
So check it!
They disagree about the essence of the check: RYBN said they checked it and found it can become chameitz or matzah. The Rabbanan said they checked it and they didn’t find it can become chameitz or matzah.
I would suggest that the argument may not actually be about the chemistry of the findings, and we can avoid saying this is a machloqes in metzi’us. Because if it were, it is easy enough for later generations to repeat the experiment, rather than the dispute. I think the word “iqar” in “al iqar habediqah hein cholqin — they disagree about the essence of the check”. Why “essence”?
I think they found something that wasn’t textbook chameitz-style leavening, and RYBN disagreed about where the line is drawn. They disagreed about the meaning, the essence of the check, not the results themselves.
Either way, eating chameitz is not “merely” an issur (prohibition), it is an issur kareis, a prohibition whose punishment (for the fully culpable; I am not G-d’s judge) may involve losing one’s physical place in the Jewish People by their line not being born or dying out and/or by losing one’s spiritual eternal life. So it is not unrealistic to think a custom would arise to not entirely ignore a rejected opinion in the Yerushalmi.
As for my own favorite theory, this year it’s the Gra’s. He invokes Pesachim 40b:
רב פפי שרי ליה לבורדיקי דבי ריש גלותא לממחה קדירה בחסיסי אמר רבא איכא דשרי כי האי מילתא בדוכתא דשכיחי עבדי א”ד רבא גופא מחי לה קידרא בחסיסי:
Rav Papi allowed the exilarch’s manor’s kitchen staff to thicken the stew with lentils.
Rava said: is there one who permits this activity in a place where servants are common?
Others say: Rava personally allowed lentils in the stewpot.
The two variants of describing Rava’s position agree in content. The first says it in the negative — when dealing with kitchen staff, one shouldn’t allow cooking with lentils. The other in the positive — when dealing with himself, Rav would permit.
Still, we see there is an opinion in the gemara that prohibits cooking with lentils, at least by people less likely to be careful. If a community worries that its observance may be closer to the meticulousness of the exilarch’s kitchen staff than to Rav Papa’s, following this gemara would have them avoid cooking with lentils and anything else that shares this concern. The Gra suggests this is exactly the minhag of avoiding qitniyos.