I'm confused. Is was under the impression that in fact this is the "bind pose approach" -
these weight positions are provided only in bind pose(scratch that, they are pose independant, they only inform about mesh "volume", combined with bones, bind pose or not, they give the final result) and I also have bind pose skeleton provided. So how do I get rid of these weight positions? What's the usual approach here? Right now I have bind pose skeleton but in fact I don't use it while animating. It's only helpful when "unpacking" animation (skeleton) frames but it looks like there's a reason it's there. I have no idea if Doom3 uses these weight positions in shaders. I just followed mentioned tutorial and ended up here.
I animate MD5 meshes in a way C0lumbo implied. Post multiply your animation pose matrices with the inverse bind pose. Then you can just send the bind posed vertices to the GPU.
I'm not sure how animating is done in Doom 3, but maybe it is possible that they did not use GPU skinning, because they needed the transformed vertices for constructing shadow volumes. Then it should be faster to have the vertices in weight space so that post multiplication by inverse bind pose is avoided.