Here's the scene with the bones zeroed out and finalik working properly.
I just went into blender and the bone rotations there look fine, all zeroed out. Just a slight rotation on the left leg, but that can't do any harm. Bone orientations also look very neat, all-in-all a fine rigging job. Fbx is exported just fine too. Without the locomotion and bridge script, things work fine.
I just fixed the avatar configuration by zeroing out the spine, also took out the -90 rotations. And brought the ORG-hips to (0, 1, 0) position. Also applied the same on the prefab's model of the character. Without the locomotion and bridge script, and zeroed out values, the alignment on the
Atlas prefab is absolutely perfect.
With those scripts, and the avatar's bones having zeroed values, the head is still slanted and things don't behave well at all.
Without those scripts, and
with the avatar's bone rotations zeroed out, the head aligns perfectly...
Also, just the pure Atlas FBX dropped into a scene with all of its unfixed original bone rotations and -90 blender rotation works perfectly fine as well with a FinalIK LookAt.
So it could very well be it's not the bone rotations at all... Or it's both... But it surely is code-related.
On the Atlas Prefab, without loco & bridge, zeroed out spine/neck/head