At the moment, adding users via a provisioned group that has app access bypasses the app invitation email.
However, if an existing provisioned group with members is granted a new app access, the existing group members get the invite emails in bulk.

Suggestion
Disable invite emails when granting app access to existing provisioned group with members

Further Suggestion
Add details in the UI that warn admins that adding groups to an app will notify users in the group.

Workaround
Grant the app access to an empty provisioned group and then add members to the provisioned group to prevent the invitation emails from being sent out.