Whether it is commercial or open source the solution has always been to explain to the user and ask informed consent. No one is so busy or so stupid that they cannot read a small para of text (possibly linking to a detailed document if they're so interested) and press one of two/three choices at some point during system setup or usage. Of course these permission prompts tend to grow out of hand as we can see from commercial operating systems but this is something Linux distributions can do better since nearly all software just want usage data and not user data like their commercial counterparts do.