M2M JWTs and Flutter native application JWT with scopes

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No, that setting adds permissions to access tokens only - If you need permissions in ID tokens you’ll need to do so manually:

How to add Roles and Permissions to the ID Token using Actions?

Problem statement Is it possible to retrieve the user’s Roles and/or Permissions and include them in the JWT Token? Solution Yes, it’s possible to retrieve the user’s Roles and/or Permissions and append them to either the ID Token or Access Token. To do so, you must use a Post-Login Action script. 1.1 Roles When adding the user’s Roles to the token, call the event.authorization.roles property and add it as a custom claim to the Token. Please see here on creating namespaced custom claims. Be…