Best practices for using global navigation in the SharePoint app bar

SoulFroys Thanks for reaching out. At this time the SP app bar is global across all sites so there is no way to enable to only a group of related sites. A potential alternative is to leverage audience targeting in the global navigation to target individuals in the separate companies, but the global navigation logo entry point will be the same for everyone. If you're not already, I recommend using SP hub sites for the individual companies within your tenant and that also provides navigation across all the sites associated to the hub. 

Mirek_N including you as well for my note above around alternative approach and mention of using SP hub sites