Can I control the permissions of pre-installed "system apps" in Android Marshmallow? I am really excited for the permission control feature available in Android M. I am considering buying a phone that supports this OS just for that one feature.

However, I am concerned if I will be able to control permissions on the "stock apps" without rooting or flashing my device with a new ROM? Even a Nexus will come with stuff like Google Maps, I am sure. So will I be able to control what Google Maps has access to, for example? What about Samsung devices and the egregious bloatmalware they package with it?
When using apps which require certain permissions for the first time, the app asks you to grant the permission, which happens with stock apps too. If it doesn't, then permissions for stock apps can be managed in the App Permissions section of the Settings.