Where I work we apply torque stripe/seal to any torqued fasteners. Until your post I never really thought too much about where we apply it. However, I can tell you that we always put the torque stripe between the bolt head and the "base material". But I guess that's just for bolts going into nutplates where the nut is not accesible. When we can get to the nut, we torque the nut and stripe from the nut to the washer then to the base material. I've never seen torque stripe applied to the protruding bolt and nut only.
Sorry for rambling. Your post just got my gears turnin'.
