Yeah I noticed that too. I just figured it was too hard/the devs too lazy to program DT to only effect areas that the armor cover. As it is now I think that it's applied to the body as a whole. It would have been better if you could headshot someone in power armor and completely ignore the DT if they didn't have a helmet on.
Probably "not possible" given the way the game engine works.
Unlike some other RPGs where you can mix and match outfits, FO:3/FO:NV really only give you 3 clothing slots (body / head / face). So while it would have been nice if there were varying DT values per body part, I can see why they didn't bother. Too hard to explain to the player and it would take a dozen or two lines in the code where the current calculation can be done using a single line.
A combat overhaul, using a script extender like FOSE, can probably expand that. Maybe calculate a basic "body part A gets X% of the body slot's DT" or "the head only gets DT if a helmet is worn". Especially since it already keeps track of damage-per-limb to calculate crippled limbs. But there would be a lot of special cases for enemies that aren't humanoid, or their model has special armor on one limb and not another.