Yes and no. The right tool depends on what you actually need to accomplish.
The module supports Magento’s multiple sites functionality. I’ve seen people use that to create store fronts for specific affiliates. You can configure the module per store view. If you set the Affiliate ID parameter in the configuration you can assign all sales from a specific store as a commission for a specific affiliate.
The “Site Replication” banner in PAP should not be used to attempt to replicate a store. Use PAP’s site replication with your landing pages to give your affiliates good full page marketing templates.