I just found out that doing that does not prevent shortcuts from the extension to work contrary to what I just posted although I'm sure that when I tested this yesterday it did...:) So this is a step in the right direction.

Then I'm still left with sites stealing focus preventing shortcuts to work. Even though Vimium has an option to prevent sites from doing it, it is not fool proof. YouTrack/Upsource for example insist on stealing focus, so when I'm happily switching tabs using shortcuts as soon as I stumble upon YouTrack/Upsource I have to grab the mouse again :'(.