First, the bond between the primer and the topcoat is ensured since the products are in the same family. It is the case that sometimes products don't "like" each other. For example, epoxies typically do not bond well to urethanes, but urethanes bond well to epoxies.
Second, in the event of a deep scratch the primer coat will continue to provide a very high level of chemical resistance. Please contact us top discuss if this is the right option for your application.