In the SpineFixationWithForceDependentKinematics:
1- The joint reaction forces of L3L4 during flexion movement represent all the forces from all muscles in the system including the weight or only muscles acting passing the L3L4 joint?
2- Are the muscles that don’t pass the L3L4 joint such the ones with fascicles ending at L3 or starting at L4 have their forces calculated in the L3L4 joint reaction force?
Sorry for slow answer.
A1: short answer is yes. a joint reaction force will always be a result of both muscle contractions, masses external loads etc.
A2: Not sure i understand the question, but here are some background info. In AnyBody the reactions forces are found together with the muscles forces, there are no intermediate step of finding moments then going to muscles. So if a muscle do not cross a joint you can say that it will will not directly change the forces in the joint, but it may change the moment balance and some other muscles which do cross the joint might change.
Hope it helps