I ran into the same issue, and I don't see a way to specify the publisher identifier info, we run into throttling errors all the time and pulling down data can be delayed greatly.
See microsofts response below:
The throttling limit are calculated per PublisherIdentifier. If you don’t pass a PublisherIdentifier parameter a Global Identifier 00000000-0000-0000-0000-000000000000 will cause throttling frequently as it will calculate resource usage based on all calls that do not pass a PublisherIdentifier. And this includes calls from other tenants as well.
From the error message I see it looks like you are not passing the PublisherIdentifier parameter so the call uses the global PublisherIdentifier 00000000-0000-0000-0000-000000000000.
To fix this you need to pass a Query string PublisherIdentifier=<> to each and every call of the management API.
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