So, as I understand. You've got App A, which is available at ABC.com and XYZ.com. So 1 app and 2 custom domains.
The SSO module is able to provide 1 metadata file for a SP, but you need two, one for each domain.
I don't think this is a common setup, at least I haven't seen it before. I don't think this can be done out of the box with the default SAML/SSO module. So you might need to customize the module (change the java code perhaps), and the ability to add multiple SP's..