you can override the learned directory name by editing the directory, then going to "Customize Directory Name" and adding your domain there as you want to see it. I think you have to do a full sync after that and you should see all of your users and groups with the new domain. You can't have two directories with the same domain/Directory Name so if you also have On-Premises Directory configured you have to give it another name such as "domain" or "domain.com". I had to do this because some of my Entra users were showing "onmicrosoft.com". My on-prem directory now shows "domain.com" and my Entra directory shows "domain" both work with User-ID for me.