Sorry to bump this up -
but I ran into the same problem, and may have found something that - if anything - may give some insight into the error itself.
Mind you, I haven't attempted to re-order the objects either, but I was more concerned with being able to repeat the errors to report this before trying workarounds.
The initial error notes that three layers are assigned twice - the upper and lower neck (each their own pin/node) and the pelvis, as follows:
Layers assigned twice
15 - Neck - Upper
16 - Neck - Lower
14 - Pelvis
This error comes up trying to proceed after the Spine Autorig menu.
Now, if I remove the links to the neck only (both "from" and "to" for the neck become "none"), the error changes to:
Layers assigned twice
14 - Pelvis
Now, if I deselect the pelvis, I can proceed to the next menu, "Tail Autorig," where, unsurprisingly, the "hips, pelvis, abdomen" is assigned to the Pelvis node on that menu.
However, I can also go back to the Spine Autorig menu, and deselect the Neck and Spine/Torso/Chest/Thorax nodes
without deselecting the pelvis, and be able to proceed forward to the Tail Autorig with no error.
For whatever reason, this combination (which still leaves the pelvis linked twice) doesn't present an issue.
Thought I'd chime in with this; maybe it'll be of assistance (I hope). I'm no coder, but it sounds like the parts association for each drop down may be incorrect. At any rate, I'm going to reorder my parts now and try it again.
EDIT: FYI: Reordering the parts did the trick.
-Kurt