When you look at a mesh in Milkshape they have the arms straight out, like if you press F6 in Bodyshop. But I'm finding that with some meshes like the attached the mesh looks annoyingly different with the arms down. Is there any way to see how the mesh will look with arms down in Milkshape?
It most likely has to do with how the mesh is weighted to the joints. The T-pose is the base, and basically is the "perfect" version. Anything else has some animation applied and could potentially be somewhat bent out of shape. If it gets bent very out of shape in Bodyshop, it's likely it's going to look worse ingame, because the sim doesn't move a whole lot in Bodyshop.
It most likely wouldn't help that much, no. But it depends why you want the arms down. If it's for pictures, I guess it could help.
The joint assignments will be the same no matter how the sim is posed in Milkshape. If you're making a mesh and want to see how it looks when the sim has arms down, then sure - having a pose with the arms down could be helpful in seeing how the mesh would look like ingame.