It's not a real domain, so you will not see it in the tool config. Any user that has the new domain stamped as part of their attributes, such as UPN or proxyAddresses, will have the value automatically sync though. The only thing you need in terms of configuration is to make sure the mydomain.com is added/verified in Azure AD/O365.
Azure AD Connect Cloud Sync, how to sync new UPN suffix?

New to M365 and trying to get our local AD to sync correctly using Azure AD Connect cloud sync. Our local AD is using "mydomain.local", so we've added a new UPN suffix "mydomain.com" to our domain, setup a new OU for testing and the users in that OU have the new suffix. The "mydomain.com" is used for our website and email addresses, we use on-prem Exchange 2016 servers and have no desire to move to hybrid or Exchange online at this time. I've installed the Azure AD Connect cloud sync agent on a domain-joined server and I've gotten it to configure correctly for "mydomain.local". How do I get the sync agent to see "mydomain.com" and have that available for a sync option in Azure AD cloud sync site? If i re-run the Azure AD Connect Provisioning Agent Configuration again, at the "Connect Active Directory" screen I click "Add Directory", but nothing I input for "mydomain.com" works. Unsure where to go from here.