The various functional "mechanism" body parts are all set as being [INTERNAL] to a generalized "mechanism" body part, which is protected by an armor body part. Internal organs are damaged at random when their parent body part is damaged enough.
So, you have to tear or break off the housing, then you can start smashing the general "mechanism" body part. Once it gets damaged enough you should start getting messages like "you bash the machine in the mechanisms with your war hammer, breaking the gears and fracturing the right arm's motor assembly"
(underlined bits indicate what parts will change based on the name of the creature/its tissues)
EDIT: in other words, it works exactly like the guts/stomach/etc do in the default creature setup, with different names and with the "mechanical housing" bodypart acting as a layer of armor.
FURTHER EDIT: and the arm thing works because if you damage FUNCTIONAL (or is it STRUCTURAL?) tissues in LIMB bodyparts it disables the function of LIMBs and GRASPs connected to that body part. At least, I think it does? You can't hold things with a broken arm, right?
EDIT NUMBER THREE: You might also be able to just use my first example, only with a single "mechanism housing" bodypart that covers all the functional body parts. I'm not sure if BP_RELATION can be used to say that a body part is around more than one other body part, I've never tested. I just suggested the approaches that I'm reasonably sure will work first.