Improve the messaging related to Directories and Resources

Scenario

 
Civi gives uses warning eg 'Directory Paths: Make them portable' and takes them off to the Directories page to fix them, and they make the changes and save them, and the System Status warning remains - so they go back and look in Directories and guess what, the changes have not been saved. Frustration builds up.

Someone 'in the know' would say 'hey I wonder if those are stored in civicrm.settings.php' and therefore perhaps hide the warning, but could we be providing a notice on the Directories page to say 'hey currently your values are set in civicrm.settings.php and therefore changes to this form will not be saved' or a msg after they try saving (so they only have one round of frustration)?