When using a custom world generator, a stacktrace is printed to the console when attempting to use an Eye of Ender. Ingame, nothing happens at all; the Eye of Ender is not consumed, doesn't fly and stays in your inventory.

(In Spigot 1.8, the Eye of Ender just pointed towards some location where Spigot believes there is a stronghold.)

Attached is the stacktrace and a very simple custom world generator plugin called 'SimpleGenerator' (both source and binary).