I definitely think visibility toggles could potentially lead to a messy document, but probably from mismanagement, just like a Media Library can become a hell to navigate without proper tags and file names. As for the misclicks, I think that simply moving the toggle to the options dropdown, where copy, paste etc. are located, would solve that issue, but that's just one of the options that can be considered 
And as for the dev case, most of the time it's not a big deal as Slice Simulator and Live Preview are enough. The use cases where they usually are not enough would be the before mentioned gradient spanning, so basically some kinds of interactions with other slices. Slice Simulator is also not enough when content relationships are to be tested, and Live Previews are sometimes not enough with detailed content, as the previews are quite small, which is why I've supported this idea of bringing an ability to the end user to enlarge them if needed.
Thanks for taking your time, I appreciate you looking into my idea! Even if all this achieves is improving existing features like releases, I'm happy that I had my part in contributing to the great product!