drewyallop,
Every action torque is accompanied by a reaction torque, Newton's third law. The wrist torque exerts an action torque on the club shaft but there is also an equal and opposite torque acting on the arms. Similarly for arms and shoulders, shoulders and midsection, midsection and hips, hips and legs , legs and earth.
One thing must be clearly understood – the internal torques generated by the golfer have eventually a reactive counterpart, small or large, relative to the earth. This reaction torque acts now as an external torque to the golfer/club ensemble and generates the angular momentum. Its is kind of strange but so be it.
The analysis shows that the proximal torques generate substantial angular momentum whereas torques more distal such as wrist torque, do less or practically not at all. They however do redistribute existing angular momentum, e.g., flowing from arms to club during the release.
Now more specifically your questions.
For the torque between mass m3 and m4 indeed there is negligible angular momentum being generated. This particular torque has a very small reactive ground reactive torque component and hence does not generate any appreciable angular momentum into the golfer/club ensemble.
The earth constitutes the reference coordinate system for the calculations.