floresta:
So we agree that when he designs his board he just leaves the pins unconnected
Yes. Unused pins should be unconnected.
or better yet brings them out to an accessible pad
A very good idea.
The enabling of the internal pull-ups could be done, if desired, by any program when the board is actually used.
Yes.
This enabling would have to be part of each individual program since the enabling is undone at every reset.
In my case, I would (clone [if necessary] and) modify the core so enabling the pull-ups on unused unconnected pins (especially ones without pads) is performed before the Sketch starts. That is, after all, the point of a computer: to do the simple repetitive tasks that we humans tend to forget.