Yes, if you configure a product-based Affiliate percentage, that would override any Common Affiliate percentage you had otherwise configured, and you don't even need to enable the product-based Hop Link, as a Common Hop Link will credit Affiliates for the proper percentage.
The reason the settings are in separate places is because the Common settings were recently added, so we had to retain the older product-based settings as they were, and it didn't make sense to try and add the Common settings into there. Perhaps we could consider eventually adding the dropdown menu for product-based settings into the new Affiliate Program Settings screen itself.