SPO restricting accounts to specific site document folders

Is there a reason that you are having that company use an internal account? By doing that it’s making this a whole lot more complicated as opposed to just sharing with them like you do normal sharing. Because once you make them internal you can no longer use the everyone security option so unless Only those companies and a few select people can access those folders breaking inheritance won’t do anything if you still need the whole org to access the files.

You would have to have something like an internal employee type group with everyone in it to use in your site instead of everyone then add the other users onto those folders or just share with specific people too. Multiple ways but you will have to either do the group for all internal excluding those that can’t see their stuff or use external sharing with accounts not inside your org.