I spoke to apple support over the phone - there is a file he pointed me to which lists all permission messages which can safely be ignored - those in red need to be urgently acted on.
All my messages fell into the 'ignorable' category - why do they bother to list them during repair/verify disc!.
Ha! What a cop-out.
I have the same questions when I call tech support and have to enter my phone number so they can "find" my account and direct me to the appropriate staff and then the supportzombiebot asks for it a 2nd time.