Greetings Ben,
This feature was added intentionally keeping mind the security features where all users added in Everyone Organization should not have full visibility.
PTC designed Asset Advisor for use by a Maintenance Technician, designed Controls Advisor for use by a Controls Engineer and designed Production Advisor for use by a Plant/Production Manager.
There are typically “regular” (non-admin) type users and then “super” (admin) type users. Admin type users typically have write/design permissions and regular users typically have read/run type permissions.
From an operational perspective, a best practice may be to understand the different types of users and permissions needed for those roles and set-up accordingly.
Each business would have to determine what is best for them from an operational and security aspect.
They may wish all users to be added back in the Everyone Organization granted all visibility or assess user roles and the specific permissions that should be granted for each of them.
Now the scenario where you want to add users in Everyone Organization is that when you want to invoke the service of thing which do not have visibility for that user.
Thanks,
Himesh Rajpal