Deployer does not fully support the Claim-based user authentication. However, that does not mean that Deployer will not migrate the contents to the claim-based site collection. It does allow you to migrate the contents to the claim-based site collection but in order to take advantage of claim-based users in target Site/site collection or map the source users to the target claim-based users, these claim-based users need to be added to the target Site collection prior to the migration and then only Deployer can read target claim-based users and allow you to map source users to these claim based users.
The reason behind Deployer being unable to add claim-based users to the target site on it own (during the migration) is because Remote Service cannot be operated using the claim-based users. Only the NTLM user or Windows user can run the Remote Service currently and the Remote Service is the component which is primarily responsible for reading/writing the data on target SharePoint. Thus, comes this limitation.