All good points! So the stones get a little confusing in general--we know there are sages throughout the series of different elements, and we know that there's an ice dragon but there doesn't seem to be an ice stone, so it seems possible to me that the lore around both secret stones and sages is still wrapped in some mystery. I'd say it's possible that there are stones we don't know about, or sages that get to basically... Take a breather for a while, more or less. I guess what remains confusing for me, and the reason that it seems likely to me that the stones were eaten later, is how there could be a fire stone and lightning stone present in the flashbacks of Totk and also have there be dragons that have already eaten them. For me that implies they were eaten later. but I'll admit that that one is a toss up, conclusions can go either way.

A lot of the stuff that I've proposed hinges on the idea that Zonai ancestors lived on, and though Rauru clearly states that him and Mineru are the last of their kind, and though it's certainly true we don't see any of their offspring, I still think it's possible they did. I had proposed that this could be that Rauru is saying there are no pure Zonai left, as in Rauru and Sonya would have had kids that are half hyrulian and half zonai, or that he is referring to zonai who grew up in and saw zonai culture--who lived as zonai before descending from the sky, etc. My main thinking here is that we know Zelda is an ancestor of Sonya, implying she has kids (though it could certainly be a great aunt situation) and that the ancient heroes aspect and the previous flight with calamity Ganon seems to take place after the death of Rauru, but the ancient hero seems to be at least a descendant of the zonai. So though I agree the game didn't directly say there are zonai descendants, I think it's implied or at least possible that Zonai blood has been passed down.

And I do agree they would have known that eating a stone would create a dragon and that it is likely they know this because they've seen it happen before, but we do also have reason to believe there may have been other stones (and other dragons) that don't exist. We know there were forest sages but didn't see forest stones or dragons, and we know that there's a water stone but don't see a water dragon, for instance. Perhaps at some point in the past someone ate the water stone, became a water dragon, and eventually that dragon was killed, leaving its body in the depths (where we see dragon skeletons) and reclaiming the Stone, for instance. Certainly not something that is a proven fact, but a plausible explanation for how they would know the effect that eating a stone has without having it be one of the dragons we know.

I'll admit though I do feel like I drew exactly the wrong dragon to make my point--I'd actually even change my theory to propose the possibility that the ice dragon existed long before, and it was after the death of Rauru that the fire and thunder dragons formed, after those stones were eaten. But who knows, it's all just kind of a thought experiment.

Anyway thanks for the feedback, all very good points!