im2smart4u: you're right there, but there is also the promotion factor, for instance, as well as simple transfer within the military "departments", so to speak. We don't know whether ridgeless bone mask is of inferior rank to the ridged one, or whether it simply refers to a field commander of equal rank. Thus, Noctus could've either been promoted through deeds unknown to us or transferred to due to, say, loyalty shown, to Nelis. Thus, it's possible that Noctus was there. On the other hand, the Somnus scene has no interaction between one of the Shadow Guardians recognising the Main, so he might not have been there (then again, Tastidian, his superior, was speaking, plus the Main was the enemy, and it would've been a bit strange to speak out of rank and to the enemy). yogc also provides a good alternative- we don't know how many Shadowlings were killed before wartime action was stopped during the time when the Palace was stormed (as Nelis was too busy defending herself) and when the Shadowlings armies stopped the fight: Noctus could've been killed-in-action during that time period, if he was revived in the first place.
This also birngs up another point not really highlighted, but sssss (I think) brought up the point about why Nelis can't simply revive Gen Drakeye if he gets killed on Lake Alto? And why fate, but not Nelis intervenes to save the Main? It was postulated that if the person is too important for the flow of history, then he/she cannot be revived just like that, not even by Nelis, as it affects too many people around the world.
For the Gen Darkeye part, my explanation can be that if Spriggats were to overrun the Shadowlings, then they would most likely capture Gen Darkeye, use deep scanning on him and prevent him from commiting suicide (is that even possible for Shadowlings?), thus extrating valuable information from Gen Darkeye. Also, why wouldn't Gen Darkeye simply kill himself (apart from the ethically dodgy part of leaving his troops) and then let Nelis revive him? Maybe she cannot revive those who voluntarily take their lives? Hence, the Main is forced to save Gen Darkeye, as there is no other plausible alternative.