Well, no; there's two problems now. The first one is that your browser will handle click events on invisible and near-invisible layers. The second one is that your browser will allow click events to flow through opaque and near-opaque layers.
The problem is not that events bubble, but that clicks fall through visible layers to lower ones and get caught invisible ones on top of what you intended to click on.
Invisible click areas as you called it are not the same as multi-layered click targets imho.
This is just another brick in the wall. The web is /not/ a platform that's friendly to new implementations, and it never will be; the complexity that's constantly being added ensures this. It also means we're all going to have a lot fewer guarantees of anything like sane behavior when using the web in the years to come.
