I do find myself wondering why Yoshi-P never thought to seek clarification as to why Emet-Selch was so popular...

I suspect that by doing so, he would have been forewarned of the pitfalls to avoid. Another problem is the desperation to make almost every antagonist and villain tragic and sad. It worked for Emet-Selch but that was due his circumstances being so compelling. He was forced to do bad things because his loved ones were wiped out for dubious reasons. Hermes...basically threw a fit and decided to risk the extinction of all life but then we're meant to believe that he did it because he...loved all life? That just doesn't fit. If the game was more honest about him being unhinged and having snapped rather than having a point then that'd be a bit different. Though we still get attempts to try and pretend as if what he did was in any way acceptable.

A good test, I suspect, would be to propose the actions of such a character to be inflicted upon the Scions, City State leaders and all of their loved ones.

Would they accept what Venat and Hermes did being inflicted upon them? No? Then it's probably not an act to glorify then, is it?