RE: Where are Navigation Pane options stored?
Code and metadata (including menus) is defined once for the whole installation and shared by all companies. What can differ is security setup in different companies.
It seems that your goal is having the same permissions set up in all companies, but you don't have it now for some reason. That's the direction you should follow and leave the incorrect expectations that each company has a distinct copy of the menu stored somewhere.
By the way, I find the list versions in each of your post rather distracting and not very useful, as it doesn't make clear even whether you're talking about AX 2009 or AX 2012. Consider making it smaller, removing line spacing and visual separating it from your actual reply, if you don't want to get rid it completely.