We keep disabling Focused Inbox for two main reasons;
1- It's Microsoft proprietary. People use other devices and apps to access their email, when checking email on say iOS mail FI doesn't work, so all that clutter is still there in their inbox. Clutter is recognized by every platform and app. If the solution is "just use the Outlook app" that is unacceptable and will never, ever happen.
2- Focused Inbox sorts the inbox by default, so teaching it to be accurate is incredibly intrusive. It takes weeks to get the system set up, and in that time the user is constantly looking for email that should be right in front of them. Clutter, by contrast, is passively taught and is done at the user's convenience. That difference in user experience is absolutely huge. Sure, they end up working the same in the end, but the difference in interface is everything.