Of course, we have the similar problem that if we make an entry set
    with add-hook in .emacs untouchable, then the user can not undo it
    for the current session any more either, even though this is feasible
    and safe right now.

That is a good point.  It is harmless to change any value
just for the current session--the problems arise when you
try to save the change.

That creates a problem for solutions based on changing the way the
user edits the value.  However, they may not be insuperable.  One idea
is to offer the user a choice of two representations to edit: the
"safe" one that allows saving the result, and the "raw" one that
allows setting but not saving.

      Referring to
    something set in .emacs as "Set for the current" session would be very
    confusing because things set in .emacs outside and inside the
    `custom-set-variables' form are set in the same session.

I agree.  Perhaps "set by .emacs" should be distinguished as
a state.


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