Yes, IDE support would help developers find the method that is being called. This is already quite a problem given we have complex class hierarchies and interfaces with default methods. I'm not sure I see the need for an annotation though.
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 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.
This whole what-if scenario is a complete non-issue. Many other languages do this out of the box and have no issues with it.
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.
Literally any code you write could interfere with some non-standard extension plugin, this is all pointless hot air.
Which is one of the reasons not many use non-standard extension plug-ins for their compilers.