Setting shorter descriptions via the setting on an individual exposed filter in Views does work - which makes sense because views is using $widget->description, as opposed to how BEF adds the #description to the rendering of the form element itself (View's $widget->widget).

I'm guessing there's an additional step needed for theming, but I can't figure out how the $form['field_FIELDNAME_value_op'] and $form['field_FIELDNAME_value'] bits are rendered together. I'm betting the secret can be found in views_plugin_exposed_form.inc, but I haven't found time to understand the Views plugin system yet. :)