I feel like we're talking right past one another. The ultimate reality is that annotation processors are pretty terrible for implementing functionality that a lot of Java developers depend upon. You could say annotation processors "weren't designed for that", but then you're just agreeing with me. This is sad, because arguably something quite similar to annotation processors could make the jobs of all of these developers a lot easier, instead of having them falling back to other mechanisms.
If your concern is integrity by default, why not just add yet another flag for can-muck-with-the-ast-annotation-processors? Or we can continue with the status quo.