Unable to configure Custom Domains on B2C so cannot set the correct Application URI. Causes mismatch on SAML ACS lookup

I have created a SignIn Customer Policy based upon the examples for LinkedIn and SAML that I have been able to find. I have correctly configured my SAML based app and it is redirecting to b2c site as expected to start the UserJourney. However currently it is failing the initial stages of Authentication with the following error:

The specified error:

              "Key": "Exception",
              "Value": {
                "Kind": "Handled",
                "HResult": "80131500",
                "Message": "The specified assertion consumer service URL https://test.xxx.com/api/1.0/sso/12345678/acs/ is invalid.",
                "Data": {
                  "IsPolicySpecificError": false
                }

Note : The specified endpoint above does exist and is the ACS endpoint.
We have a correctly running SSO setup which is connecting to the Azure AD service and correctly connecting via the same App. This is using the same URL but with a different unique ID i.e.

URL https://test.xxx.com/api/1.0/sso/AABBCCDDEEFF/acs/

The problem is to do with the Issuer value. By default we send the apps metadata URL as the Issuer. This does not match the Application URI and it is not possible to set this to any domain except the B2C domain. Currently unlike Azure AD where you can set Custom Domains and as such correctly allows our app to auth using SSO.

Why can you not set up Custom Domains as you can on Azure AD, from reading the docs they are based on the same technology, seems a limitation to me.