One of the things I find most fascinating about Sothis in Three Hopes, despite the limited amount of screen time she had in that game, is that I can't help but think: what if Sothis was a tyrant in the past? Now, 'Fortunes' weave will probably make this ask age like milk; it's coming out in September, but I cannot help but think about it. The way she acts towards Byleth—she treats them not as a person but as her vessel. She kind of is tyrannical towards them and doesn't really value human life. In the bad ending of Scarlet Blaze, she doesn't care if she is responsible for the deaths of millions just to kill one person. In a way, if you really think about it, Sothis, out of any of the characters in Three Houses, needed the time in the academy the most, because I don't believe she was a good person before her death. Maybe that is why Rhea acts the way she does—because she learned it from her mother. Japan hated Three Hopes, especially for its portrayal of Sothis, and I actually like her portrayal in Three Hopes. I actually think it adds dimensions to her character in Three Houses, and that Byleth does not just change the lives of the Three Lords they choose to teach but also Sothis herself.
So this, I think, in three houses, choosing to give up her second chance at life in order to save Byleth was her redemption for her past. I like to think that she was not a good ruler when she was alive. If anything, I actually think this would have been an interesting thing to explore in your hypothetical Silver Moon route.
I think in a sense you are right but I don't really view her as a tyrant. I think its more that she is ultimately really a god and subverts the very pacifist loving mother goddess archetype or the love and redemption new testament idea of a god and instead feels more like a very classical godlike figure. In the western context the best comparison would be the god of the old testament, but I think it also fits the classical idea of creator deities across mythologies as well.
She is certainly a loving goddess because she created the nabateans as her children and gave herself up twice, one time to restore the life in Fodlan and the second time to safe Byleth. But she also has a vengeful side, the side that flooded the land after the agarthans waged war against her and that will cause death and destruction for Byleths sake. And the overarching theme with Sothis darker side is vengeance, not tyranny. The fallen Byleth alt in Heroes is after all called the Vengeance Vessel.
After all, contrary to some interpretations we can assume that the ancient agarthans provoked Sothis wrath. Their own text in the shadow library has them admit that they were destroying life and that Sothis was bringing salvations to the beasts of the land, the sea and the sky. So I think the question would be less if Sothis was right in bringing down the agarthans and more if she went too far in her vengeance. As a goddess she also seems to represent nature in this context, as opposed to the agarthans who represent unchecked technological progress. Which is a common enough trope in japanese media. Think Princess Mononoke and Mononoke. If anything the conflict never ended because it lacked a mediator, like Ashitaka and San in Princess Mononoke were able to mediate between man and nature or Aerith in FF7 who protected the planet but spared mankind. Thats how I read her, her evil side is unrestricted vengeance.
I didn't really go into it with my hypothetical because I don't consider it that important to Rheas narrative. It probably would be more important if there was an agarthan recruit with supports between them and a nabatean that focusses on mediation and ending the circle of violence between their people.

















