I just discovered this menu yesterday. I found it by right clicking on one of my extensions. Is there an easier way to find this? I know it's under Tools, but it's not an intuitive location. I thought that Preferences was all the options.
TheAllegedGenius Extensions are not part of the browser options as they do not ship with the browser. There is Tools -> Extension, there is WIndow -> Extensions and as you've found the menu is referenced from extensions themselves. I am not sure the visiblity is problem, more maybe a habit?