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I haven't played the sixth installment and won't, on principle. (I won't continue further, as it would be a deviation from the topic. All I'll do after finishing this part of Heroes is read a summary – and even then, only for the sake of Ashan's story.)
Regarding the number of races in the Gray Alliance – yes, not all of them. But I slightly disagree; I mean not the Gray Alliance, but simply the alliance. During the first Eclipse, humans, dwarves, mages, elves, and orcs fought against the demons. Mages and orcs did appear later, but the rest are indeed Ancient races, i.e., those who lived in Shantiri.
Sar-Elam appears later, but not significantly enough for the Shantirians to completely disappear. I think that by "Ash's servants" in the context of Ashan's story, they meant the Shantirians (or I read it somewhere), which is obvious, as the schism among the followers of the Seventh Dragon occurred shortly after, so they couldn't have hidden the skull yet. Then, most likely with the arrival of Kha-Beleth, a brutal hunt began for the remnants of the Shantir, as a result of which they were forced to pass the skull on to others for safekeeping. Well, and then the story of the Skull becomes known.
I remembered something else – regarding the Temple, it's quite logical. The Shantirians decided not to risk carrying the skull with them anymore, so they either left it there or gave it to someone for safekeeping (I can't remember who).
I'm talking about your Armageddon specifically. Nothing is said about it during the Ancient Wars.