I am the owner and administrator of my Office365 and SharePoint Online.
In Sharepoint online I have the OOTB root team site and I am the Primary site collection administrator. The owner groups of this site is empty. I can administrate this OOTB root team site without any problem.
I have created a modern team site and added my account to the site with full control. But, every time I try to manage the navigation under Look and Feel I get the message "Access Denied".
I am want to show a subsite that I created, in the modern team site, in the main navigation but nothing seems to work.
Managed Navigation is not supported in modern pages yet. But some things I've noticed you have to explicitly add yourself to the site collection admin for things to work. That is a classic mode setting so that's probably why. To add that you must connect to SharePoint Online powershell, and use the set-spouser with the -issitecollection switch to add yourself to a group based SharePoint site as a site collection admin.