You might want to try out `customize-face(-other-window)' and see how
it handles face aliases. (This behavior has been changed relatively
recently.) I believe that I will adapt `customize-variable' and
`customize-variable-other-window' to follow the new
`customize-face(-other-window)' behavior. (This is not done yet.)
I do not know whether or not it is important for `set-variable' to be
consistent with that. Maybe not. I just wanted to be sure that you
are aware of the `customize' situation.