Auto provisioning is a feature in Defender for Cloud. It does allow you to collect Windows security events. As long as MDFC is pointed to the same workspace you can configure the setup here if you like. Just make sure the correct workspace is linked. Though this is an uncommon choice.
I recommend using the Sentinel connector instead to avoid confusion. The auto provisioning settings are rather obscure. If you are collecting the data for Sentinel, other operators will expect to see it there. Soon you may also consider using the AMA agent and the new data ingestion filtering. Which will also be better to visualize and manage in Sentinel.
To your main question, each workspace will send a separate set of instructions to the dual-homed agents. The data should not overlap and you can easily verify this in the logs.
I recommend using the cost and usage workbooks to monitor the ingestion volume and cost after enabling event collection. This is one of the top feeds in terms of cost. Also consider that security events are the result of your audit policy configuration.