Well, let me elaborate on what I did. I used a txt editor to change the reference for the GLA in the model file from humanoid.gla to humanoi1.gla. I also renamed the modified GLA file to humanoi1.gla.
This resulted in the dooku model using the modified GLA, whilst all other models still used the basic humanoid.gla. All the animations worked, but as I said, the saber and other weapons did not align to the tags.
Its possible that my crude editing of the glm file resulted in the tags being lost.
Maybe if someone made a model from scratch that used the alternative stances, we could see if its possible.
The reason i did this was because I really wanted dooku to use his proper stance, without overiding the animations for the rest of the game.
Anakin: "Don't worry master. It would take a human sized orange tanned fish with floppy ears and a racially questionable accent to make ME turn to the dark side!"
Obi-Wan: "Where's Jar Jar"