So Trojans are apparently the twisted spirits of those who got lost within the Clockworks, and they are Fiends. Yet Lord Vanaduke, who has almost the same origin, is apparently considered Undead? Maybe I'm just missing something but I've looked through the backstory on the wiki and I can't see any mention of Vanaduke dieing before Almire became the Firestorm Citadel.
(although Vana is weak(ish) to piercing, so maybe he is a fiend and we've all been mistaken)
Knights simply got corrupted. Fiends are evil things but they have 'life' (look at devilites, greavers).
We assume Vanduke actaully died and resurrected, zombie style, wich means he's technically an undead.
Another excuse is that Vanduke was not a spiral knight so whathever turns us into trojans works in a different way on him.