It's possible that non technical users would change the include/exclude folder setup to be not in their best interest. Not all users are aware, for example, that ~/.config is where their configuration files are. Or that ~/.thunderbird is where their email is.
So if they choose a folder setup that doesn't include those folders, perhaps warn them in a nice way.
One idea we had was to have a little label appear if the user did this that would say something like "Hey! I noticed you're trying to configure Deja Dup! You did it wrong."
Which folders might we warn about?
This idea might be obsoleted by a nice way of presenting such items as first-level citizens (see the More Than Folders proposal).