Thank you for your patience. I have reproduced this issue in my lab.
The behavior is, once you configure any custom roles to the application in Entra ID enterprise apps, by default there is a app role claim that gets added for application. You don't need to add the custom claim separately for app roles.
I have reproduced this behaviour in my lab and this is by design.
As per your query above you wanted to know on how you can remove the "http://schemas.microsoft.com/ws/2008/06/identity/claims/role" claim from application?
I have reached out to our PG team to get information on the same as we are not sure if there is any way to remove some of the default claims.