It may not be simple (although, let's face it: How difficult is it to open the relevant pages of two books, put them next to each other and look up which advances do not appear in both of them?)
You're making a huge assumption that each advanced archetype clearly derives from one of the basic archetypes. I would say this is incorrect. Consider the Khorne Berserker. It could be argued that it's Champion, Chosen, or Forsaken since it has elements of all three. I instead contend that it's none of those but something unique.
There does seem to be a lot more variety with regards to the Khorne Berserker, now that I look at it. Remarkably, the Thousand Sons Sorcerer is literally a duplicate of the Unaligned Sorcerer. But with regards to the Khorne Berserker, it does appear that treating him as a distint Archetype actually does make more sense since there is not a great deal of overlap with any one distinct Unaligned Archetype from the Core Rulebook. Additionally, a little bit more of a careful reading, the Tomes do actually state "four NEW character Archetypes" (my emphasis, page 26 in Tome of Fate and page 24 in Tome of Blood).
So, I backtrack on my previous statements, but not for the reason of "simplicity", as I always prefer realism to simplicity (even though the rules are flexible to allow for both cases, take for example the case of ammunition as stated in the Core Rulebook).
However, I still think it's unrealistic that the Alignment counts should all be 0 so that a Khorne Berserker or Thousand Sons Sorcerer could become Unaligned without purchasing any Advances at the next Corruption Point threshold. Without any clarifications from FFG, the most reasonable option to me (and closest to realistic situations) would be to set the start the Alignment counts at (5,0,0,0).