Yes, mixer_3d is rotating STL files. As you pointed out in usr1_des.f:
! Rotate STL files
CALL Rotate_STL(is_1_group_id, 'Z', cyl_center(:), rot_angle(1))
CALL Rotate_STL(is_2_group_id, 'Z', cyl_center(:), rot_angle(2))
Yes, mixer_3d is rotating STL files. As you pointed out in usr1_des.f:
! Rotate STL files
CALL Rotate_STL(is_1_group_id, 'Z', cyl_center(:), rot_angle(1))
CALL Rotate_STL(is_2_group_id, 'Z', cyl_center(:), rot_angle(2))