I think you miss understood. If the OS becomes the arbiter of what can and cannot be accessed; it's a slippery slope to the OS becoming a walled garden that only approved apps and developers are allowed to operate. Of course that is a pretty large generalization, but we already see it with mobile devices and are starting to see it with windows and Mac OS.

I don't think we should be handing more power to OS makers and away from users. There has to be a middle ground between wall gardens and open systems. It would be much better for node & npm to come up with a solution than locking down access.