Bonds, voids, and clashes block actions like bands, segment info, segment selection, etc. Could these and any other visuals allow actions on what is beneath them? This also includes actions on empty space. For example, can't click and drag to rotate/move the view while the pointer is on a void.
I think it has something to do with the fact that they provide an informative tooltip explaining what the thing (void, clash, etc) is. I agree that they should provide click-through capability, but I'd like to add that I don't think the informative tooltips necessarily need to be removed in order to do that. Maybe just hide the tooltip once you click, and also dim/reduce the opacity of the clicked-through thing so that it's clear that your clicking isn't interacting with the void/clash/etc