I am a happy user of Permissions as well. And while I like it as a hack, I use it with full understanding of consequences of disabling random permissions in Android apps.
I also understand Google's position. This feature has capability of breaking apps in various ways. It makes it much harder for app developers to test and deploy the apps.
If the app requires some permission and it gets disabled, suddenly some OS calls will fail and the app will usually not be able to handle it. In best cases it may not matter, in a lot of cases it will cause crashes, in worst cases it will cause user data corruption.
For feature like this to be fully supported whole Android permission model would have to be upgraded with 3rd state, in addition to permitted and denied states for each permission it would have to add "optional/user" state and app developers would have to test with that setting on and off. This would also explode number of test cases so I don't expect any developer going for it. So disabling permissions will always be a hack and a testing/developer tool.