Thanks for the help, much appreciated.
I ended up creating a data set via the API and making a job that exported all the custom identities used on the profiles.
Not entirely sure what other options there are to XDM Individual Profile Union Schema but since this is a system schema I assume it is the only schema that should be used in a case like this.
For others looking to see how it is done go to:
Profile API will help you get this information, All of your identities (as an array) part of profile will be available including multiple CRM id.
Thanks for the answer, do you know if this can be done across all profiles or is it per profile I would have to do this?
I have just looked through the Profile API documentation and I can see I can access entities or even list of entities through the API but I am looking to see across ALL entities with more than one identifier value on a specific identity.
Maybe creating a target dataset and creating an export job would be the solution like @Danny-Miller writes?