I mostly agree, but every now and then there is actually a good reason to override/re-implement them. For example, let us say you are using virtualized components [0], so all available elements have not necessarily been rendered to the DOM (making Control-F useless).
I would still argue in these cases that the site shouldn't override the built-in keybinds. Maybe a custom search field/button, and maybe a custom keybind. But when I press Ctrl+F, I always want the same type of search to be initiated. Otherwise, there is no consistency, and efficiency suffers.
[0] - https://github.com/bvaughn/react-virtualized