The compute fep acts on the pair interactions that are specified, so the wall/reflect should not have a *direct* effect on the free energies. (That being said, if the volume option is used, then the total volume of the box is considered when correcting for volume fluctuations.)
However, I suppose the confinement will have an effect on the calculated free energies depending on your system, not related to how the compute fep works.
Agilio