A compile-time annotation could at least control whether your plugin is allowed to transform the ADT in the given context (say: for a class). Otherwise is it not possible that it transforms the ADT even when the user did not intend to? Can this be a source of mysterious bugs?
The key point is that they do it out of the box, so everyone is aware of it. As it is, it could easily interfere with some other non-standard extension plugin, for example.
The syntax tree is only transformed when instance method lookup fails. i.e. when your code doesn't compile in standard java form. You would be doing pretty well to accidentally call an extension method seeing as you either have to write them or import them.