Yes, you can apply these displacements/rotations to the end of the pipe to see their effect on the flexibility analysis.
However, a better approach would be to define an API-650 nozzle, which would apply the API-650 nozzle stiffnesses to the boundary condition (as opposed to assuming these are rigid values). Then, apply the API-650 radial and rotational displacements in combination with the settlement displacements to the nozzle's CNODE.
_________________________
Regards,
Richard Ay - Consultant