@AzureGuru Welcome to Microsoft Q&A thanks for posting your question.
Looks like you have already engaged on SO forum on the same issue,
First thing I want to understand why you want two different containers - may be the document structure would be the same - I would probably have intuitively used an approach where userId has a prefix like "anonymous_id:12345" or "signin_id:12345" if you want to store them differently and use just a single container but if you want to isolate RU/s between anonymous and signed/in/paid - then you can keep using two containers.
Regards
Geetha