As far as I know, scenarios work like mods in the sense they completely change ruleset. When the scenario is loaded, it also loads the correct civilopedia. This has been the case since Civ IV, as far as I know.
It has been the case since Civ
II. Scenarios have always been separate from the base game, and the Civilopedias do not bleed into each other.
Frankly, the mental gymnastics some people performed to try and keep multiple leaders from being a thing once Gorgo was confirmed were more impressive than the actual gymnastics we've seen from Rio this month.
Maybe that leader bingo chart was wrong? Said even after Catherine de Medici, Tomyris, and Frederick Barbarossa were already confirmed.
Maybe Greece is now two separate civs, and Pericles leads "Athens" while Gorgo leads "Sparta"? Even though they are both alphabetized under "Greece" in the leader bingo chart.
Maybe Gorgo is only in a Peloponnesian War scenario? Except that, as mentioned here, if that had been the case, we would not have seen her in the Civilopedia for the base game. That would also be a very odd development decision, considering Gorgo didn't live during the Peloponnesian War. Wikipedia doesn't mention a date of death for her, but it says she was probably born between 518 and 508 BC. The Peloponnesian War began in 431 BC. Even if we take the latest date for her birth, that would have made her 77 when that war began; it's not impossible that she lived to see its outbreak, but no mention is made of her having done anything during that war. In her time, the Greeks were far more concerned with fighting back the Persians.
Maybe Greece has a unique "Athenian Democracy" ability where they can switch rulers mid-game, so nobody else gets alternative rulers? Eh, I could actually see them doing something like that, but if they had, Gorgo would have been an odd choice to represent that. One would hope that they would know better than to cast around for additional leaders to represent Athenian Democracy, and then decide to use a Spartan queen.
Applying Occam's Razor, the simplest explanation was that the concept of alternative leaders was returning, and that Greece was simply the first civ for whom the second option was being rolled out. I never tried to claim it was "confirmed", because gamers shouting "Confirmed!" before something is actually confirmed is a pet peeve of mine. But the evidence in favor of multiple leaders was already there, and the Gorgo reveal made it vanishingly unlikely that the rest of the evidence was misleading.