Recently I've worked on improving the File > Examples menu. A pull request is currently open... and open for discussion & comments on github:
Among the changes is custom installed libraries which aren't compatible with the currently selected board go into an "INCOMPATIBLE" sub-menu at the end. Due-only libraries (ones which have "architectures=sam" in their library.properties file) are supposed to appear normally when Due is selected in Tools > Boards, and are supposed to end up on that sub-menu when an AVR or SAMD-based board is selected.
If anyone's interested in this, please take a quick look. There's test builds from ArduinoBot, so you can easily give it a try to see how the (proposed) new menu looks.