If you have a scene tree like this:
_physics_process call order would be A,D,E,B,C,F.
Now if you were, for example, to set F's process priority to -1, and D's process priority to 1, the call order would change to F,A,E,B,C,D
I tested this by creating a scene tree where every node just prints their name during the
_physics_process. According to it, Godot will process in the exact order in which the nodes are listed in the tree view, ignoring parentage, provided they all have the same process priority (which by default is 0 for all nodes).