If you set the headers on the client directly, they will apply to every request made with that client. If you pass them in the method call, they will apply only to that one request. Clearing the header from the client or not including them in the method call will then fall back to the default behavior, yes.
To be more explicit about the gap in our implementation: we have 100% coverage on read and write requests in the API (enabling this feature will hide numeric IDs on reads and reject numeric IDs on writes) but do not yet have support for requests that originate from within Asana (i.e., outgoing webhook payloads). If your app does not use webhooks, you can freely test the rest of the API, but we won’t be starting the clock for the deprecation until the entire API supports string IDs.