Of course the ISO can be only considered as a tool, a guideline. Owning a ISO certification only means, that one day of a year - the audit day - your company runs as described in the standard ?. I've got our company through the ISO9001 and 14001 and currently preparing us to achieve a 9100 certification, so I know how much it depends on the auditors experience and goodwill whether you get your certification or not. What you really do, to "live" the processes described in the standards in daily business is mostly up to you.
For the certification authorities it's kinda same - you have to deal with design objectives that are filled with recommendations and a big wishlist of how to act. Without an advisor, who has experience in interpreting these objectives and how the authorities want them to be realized you're lost!
Having a standard at least makes companies aware, that their approach might have some flaws ?. Dealing with a development crew, all with MIT master diploma for aviation design, electronics and whatsoever, me, as a purchase and supply chain guy, had to tell them, that controlling a rudder by 2 uncased wires over a length of 8m along the tail boom won't be a good idea!? In that case, a design review by a second, independent person would have helped ?. Another example: customer orders a redundant actuator and asks for a signal split cable for the input??? Okay, please, turn around and try again ??.
The more I learn about the aviation industry, the more I'm surprised by the low rate of fatal accidents ??.