Don't confuse collision and linepicks. While an animated B3D with a single mesh containing bones in fact picks only the initial pose, childmesh structured hierarchies like 3DS, X or (AFAIR) no-bones-B3D (using childmeshes instead of bones) does pick the current pose correctly, although it will return the childrens IDs, so you have to identify the parents somehow.
So do I get this right, I can't pick MD2 at all, not even the initial pose?
So do I get this right, I can't pick MD2 at all, not even the initial pose?