I have seen this type of error when the native datastore in the vSphere hosts are all the same name. The issue is a configuration in the vCenter database. Since WFA uses the Lun ID as the primary key, it is going to through an error. Personally, I don't think that the primary key should be based on a Lun ID. Two storage controllers are able to present the same Lun ID to the same set of hosts and this is perfectly acceptable. I haven't run into an issue in my testing of the Pirate Pack with multiple Luns of the same Id.
You can see which Luns are duplicated by running the sql command used by the caching table on the vCenter database directly. This will give you the entries that are duplicated.
I agree that not having the local datastores selected would be ok... but there is something else to potentially consider. If the customer is using WFA to migrate Virtual Machines from the local datastore to a remote datastore, then the local datastore would need to be available for selection. The only unique identifier for a Lun is the NAA. Two different storage arrays (same or different vendor) can present luns to the hosts with the same id.
Just my two bits... This should also eliminate an issue with the duplicate and the local datastore.