As a usability advocate I would push more for form_alter()-ing core forms when appropriate (like your example). As this makes logical sense. However, considering that most users who care about this variable are probably advanced drupal users, they will look for it first at admin/settings/YOURMODULE.
If you want, what you could do as a workaround is place a drupal_set_message() (or hook_help()) on other pages that could be affected by your setting that point back to the settings page. For example:
I think a better compromise is to put the form item ON BOTH forms. AFAIK there is nothing wrong with this technically, but I'm not sure. Bevan/ -- Drupal.geek.nz | Gtalk bevan@lucion.co.nz | YIM rudgy_m_nz | .Mac/AOL b.rudge | skype b.rudge | Twitter.com/BevanR