2 things:
1- Individual settings may have deviations from Core assumptions. Everything you mentioned is Forgotten Realms.
2- I didn't say all undead "were of Evil alignment". But a CG Baelnorn or archlich STILL radiates Evil under a Detect Evil spell. They may radiate Good and Chaos, too, but ALL creatures of the undead type detect as evil. That's in the 3.5e PHB. The Core Books also explain that some creatures' auras have to do with things intrinsic to their physical nature, not just their outlooks. The oft-vaunted Succubus Paladin? She's still an Outsider (Chaotic, Evil, Tanar'ri). So she radiates Good, Evil, and Chaos with powerful auras.
These things do not contradict each other, but rather resonate with Core RAW and what's in the BoVD. The elves of Cormanthor judged it a worthwhile sacrifice to commit the evil act of making an undead creature, because of the greater good that could be accomplished by said creature.
Again, no one said that it forced an alignment change. Just that -by the RAW- it is, immutably, an Evil act to do it.
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Deathless are different. You may want to review your BoED. Deathless are animated by positive energy. They are also TEMPORARY*. They either come into being with a specific purpose to fulfill, or they only animate in response to a threat to a place they are guarding.
Baelnorns and archliches MAY have been a prototype for deathless, but that's speculation, and there's no proof. As it stands, they are undead. And the only special exception about them is how they respond to turn/rebuke attempts.
*I know most people are familiar with deathless from Eberron. But Eberron deathless aren't actually different if you read all the 3.5e sourcebooks. Arenal (and specifically Shae Mordai) exists on a permanent Manifest Zone to Irian, the Eternal Dawn. The Deathless of Arenal require this constant, renewing stream of positive energy. That is the only reason they can last as long as they do. Deathless that accompany ambassadors to Sharn must return to this Manifest Zone frequently.