The admin/koha-preferences script is really useful. It would be even more useful if it was moved to the /usr/sbin dir This bug aims to achieve that goal.
Given how the instances configuration currently works, I think we'll have to put a small wrapper around this. That may be as easy as: koha-shell $1 -c "/usr/share/koha/bin/admin/koha-preferences $@"
This would be very useful...