Rigid Bodies are calculated after the modifiers. So the obmat that the
modifiers use may be out of date.
Currently the obmat is reset according to the loc, rot and scale of
the object at the beginning of each frame, causing the modifiers to use
a "reseted" obmat.
The patch solution was to move the sync of the rigid body transform to
BKE_object_eval_local_transform and remove all reference to the old
BKE_rigidbody_object_sync_transforms eval function.
By moving to BKE_object_eval_local_transform we can know when or not
to "reset" obmat.
Additionally, the order to calculate the rigid body was changed to
before the modifiers, so they no longer have a 1 frame delay in the
transformation (but the rigid body now has a 1 frame delay in geometry