Has anyone had a problem logging into skype for business for Powershell using a domain other than the @domain.onmicrosoft.com? Every single time I attempt to login it will give an error. I have had success when it was a client that still had the generic microsoft domain, but once it is changed to their own it will not work.
Late to the party, but have you tried adding OverrideAdminDomain with your preferred credentials? You should be able to use your email@example.com account, but tell it to attempt against the domain.onmicrosoft.com tenant.