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.
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Those are not bugs, IMO.
A lot of web Javascript would be useless if events didn't bubble, and being able to define invisible click areas is useful in a variety of contexts.
Sucks that a few people are going to be malicious about it but I think the benefits outweigh the drawbacks.
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.