The issue appears to be a dead-end configuration option in the Hybrid Environment. Microsoft does not have a way to edit the option in a local AD without a local Exchange server running in it. The Hybrid sync locks out the online ability to change the option and it does not exist in a local AD DC. The way they managed to config exchange in the hybrid environment; was to infer the settings you cannot access when the online exchange mailbox is created by looking at other fields in the user account from the local AD. My best guess so far is it is either the Proxy address field or the email address field in the user account attributes. If these are left to the defaults, blank, then when the user account is sync'd to the online servers, it's automatically assigned to the *.onmicrosoft.com domain in your tenant. My default domain is set to the public faced production domain we use, but that apparently does not apply to local user syncs, at least not yet. You can either move the user account to the correct domain online in the 365 Admin portal or set those user attribute fields in the local AD DC. Once the online user account is move to the correct domain, then assign the exchange license. The exchange server will create the mailbox with the correct domain as long as that part is fixed 1st.
To fix an existing issue, back up everything 1st, then back it up again like always. Then remove the Exchange or equivalent license from the user account. Once the license is removed, and the mailbox is gone, fix the user account so the domain is correct. Up to earlier this year, I was able to permanently delete the mailbox, Fix the user account attributes, then add a license back to the user account and the online exchange server would create a new mailbox for the user account with the correct domain. Now, it uses the old mailbox when its re-enabled, even after permanent removal. Now I have to completely delete the user account everywhere, wait an hour to make sure all the servers update, then create a new user account and make sure the attributes and domain are set before the license is added on. The only other way to fix the issue is to setup a local exchange server in your AD so you have the settings available to you locally. There are many issues with setting up a new local exchange server in an existing hybrid environment to overcome. Unless you have a few dozen user account to worry about, it may be easier to reset them individually and port the data back into the new account and mailboxes.
Good luck. I don't see Microsoft fixing this issue any time soon. Where the options are imbedded in the AD infrastructure, and how the hybrid environment engages the online config lockouts, makes it extremely difficult for Microsoft to isolate them. Most likely, we will have to wait for the next big server OS revision that is designed from the ground up for hybrid setup and configuration.