Good point, and I believe it won't happen because of these reasons:
1. Permission stored in manifest does not have ":ALLOW" section, it contains only the permission name, meaning that the application need this permission. It's basically the same as chromium's approach.
2. The permission name in the manifest are verified during installation, invalid permission name will lead to install failure.
3. The permissions will be validated by permission policy manager during installation, so it will be verified again.