There's an mp3 from -- I believe Rabbi Charlop where he quotes someone who said that you don't find the phrase breira per se in the Talmud Yerushalmi, only the Bavli. He then mentions that someone challenged this from several places in the Yerushalmi that seem to be doing something to that effect. If I understand, the takeaway was that reducing it to the named abstract concept was only done in the Bavli, but it's certainly possible that there were various intuitive halachic rulings that were recorded earlier.
(I'm not saying that's necessarily what the Encyclopedia was saying.)
This is actually not that different from something funny you'd observe in Intro to Calculus, if I understood it correctly -- first they teach Riemann Integrals, which actually prove what happens when you break something into tiny pieces and add them all up; and later they teach the fundamental theorem of calculus, which states conceptually what it looks like. In fact, the fundamental theorem was developed -- and people could solve equations and build things using it -- hundreds of years before Riemann would go and actually formally prove it.
Another possibility that could be used to answer questions of this sort (I'm not saying this necessarily works here) is that the Amoraim did not feel they could introduce concepts that went explicitly against a recorded Mishna, but as long as it could be read into the mishna (even if that was not the original intent), that was okay. The example I'd heard of this (from a "black-hat" rosh yeshiva) involved making a "borei nefashos" after drinking water. (I think Brachos 44b, but I'd have to look into it more b'n.)