A bit more playing around, and this is what I've found out so far on this method of handling creatures.
It seems I set up the base model for the creature wrong, and that's why I was having the plt issues.
Dynamic races above a certain line (appearance 481 I think it was, OTR linked me to the info I needed) will use their own plt, races below that line default back to pmh0_*.
Weapons (And likely all armour parts and impact nodes) are positioned based on the base model, not the numbers used to align and animate the creature model on the robe appearance. Races would need to be set up based on model size, likely staying within 0.1 or so for the base scale to keep things aligned properly. Creatures that don't use weapons or armour aren't affected by this obviously.
Male and female appearances both work properly, meaning there's an extra 256 potential creatures available per race letter used. Does anyone know if the other genders (both, other, and none) have useable prefixes for character parts? That'd be quite a few more slots to use for everything if they do.
So far, only a_fa and a_ba supermodeled creatures have animated properly. Likely it is a case that the basemodel nodes and robe creature nodes have to match to animate right.
Making plt files is a pain, but I do like the customizability this method offers.
Here's the kathnee from v1.4 Q as a female robe. This one uses both leathers, both cloths, both metals, hair, skin (for the lighter hair patches), and tattoo2 (for the leg and hand wraps). Some colours are set on the armour itself, some on the creature, but all 10 colour layers can be used.