If your policies are configured at the Organization level and inherited to applications then the Notifications settings for the policy will also be inherited and cannot be modified at the application level.
You can still customize Notifications on a per application basis by using roles. At the Organization level define Notifications based on Role rather than Email. Then for each application you can define who is assigned to those roles. These users or groups will receive the notifications.
On the applications where you want to customize notifications select Access.
This will show you the roles currently defined for the applications.
Identify which of these roles should receive notifications in case of a policy violation Warn or Fail.
On the Organization where the policies are defined, select the policy.
Click on Notifications.
From the Recipient Type drop down select Role and select the role to use for notifications.