I can see where you might get different numbers between measuring strain at a hingeless rotor mast and at the MRGB attachments. There are both in-plane (lead/lag and drive torque) and out-of-plane (flap) moments produced at the rotor shaft. The rotor shaft is subject to a combination of tension, torsion and bending. The tension and out-of-plane moment forces acting on the rotor shaft are typically transferred thru the mast bearings to the MRGB housing and into the airframe. The in-plane moment forces at the rotor shaft are transferred thru the numerous gear meshes of the MRGB and back to the engine power turbine output shaft. The load reaction at the MRGB/airframe attachment from torque transfer between the gearbox engine input and rotor shaft output is quite complicated.
What probably matters most with stiff rotor systems are the combined bending and torsion stress levels produced in the rotor shaft. So it would seem logical to measure these in the most direct manner practical.