Currently if you limit access to certain Mailbox stores during the autoprovisioning process, they will continue to be the only mailbox stores available during other operations. I.e. move mailbox.
This is product design. Mailbox provisioning policy limits the list of mailbox stores visible for user. This value does not depend on an operation, for example: Create or Modify or Move.
An enhancement request (TF00434703) has been created detailing the feature.
The product team will evaluate the request and this feature may become available on a future release of the product.