The animate dead spell has no mention of a soul being used for the purposes of the spell, however, when animating a zombie or skeleton within Golarion, a sliver or shard of the creature's soul is still utilized. I'm basing this on things mentioned by James Jacobs such as THIS and THIS.
As the merged body/soul of outsiders are unrecoverable when slain, is it still possible to animate their body? Is it also not possible therefore to use the more powerful create undead spells on them? Are there official examples of this being done by villains in Golarion?
Regarding creatures with bizarre anatomies -- aberrations mostly -- how are their corpses treated with respect to animate dead? For example, does an ettercap have a skeletal structure? Or is it more like a vermin with an exoskeleton? How about something like a mimic? Is there any guidance on how to reasonably judge the structure and anatomy of these stranger creatures for times when it is important?
So to quote from an odd place, the Magic Jar spell,
Only sentient undead creatures have, or are, souls.
So there is that, and it's in the core rule book.
As for anatomy, that is going to come down to a GM call.