Hello Ruben,
Did you try getting the microflow to apply entity access and then restrict the pages accordingly?
You can apply entity access from a microflow's properties, under the security group-box.
Edit: Since this doesn't seem to work - Role based homepages would be the best answer, and then for the nav you would use a single MF as a homepage link built with the pre-defined show homepage action (See below),
Hope this helps
Rolebased homepages it is;
https://docs.mendix.com/howto/ux/setting-up-the-navigation-structure#a-name-setupthenavigationstructure-settherolebasedhomepage-rel-nofollow-a-3-setting-a-role-based-home-page