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:
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?