If you start the footprint editor from within pcb_new the footprint you can save the changes you made to the pcb_new header instead of saving them to the lib.
After discussing the feature request here you should inform the developers via the bugtracker that this request exists. (Only a handful of developers visit here regularly.)
For feature requests the bug needs to be marked as wishlist.
Search the bugtracker first if a similar request has already been made (If so simply mark the bug as "this affects me as well". If your usecase is not described well, also add a comment that details why you think this feature is a good addition.)
Just a heads up, a feature request without a patch ready might take a while to be implemented. (A developer needs to be motivated enough to implement it.)
A change that requires changes to the file format (your suggestion definitely needs changes to the file format) will take even longer. (This is why i presented you with the workaround.)