Can we move the skeleton out from under the unit template and delete the "override_texture" model in there? So far with my models I've just been hiding the original override_texture in the unit template and enveloping it to the skeleton from there.

Yeah just grab bone_root and drag it to dummyroot then delete override_texture and when you bring in a new character mesh just place everything back to the way it was originally and you should have no problems.