Wouldn't "simplifying" or even awareness of the existence of such OS features be a much better solution than re-building it in a runtime?
If an existing feature is used too little, then I'm not sure if rebuilding it elsewhere is the proper solution. Unless the existing feature is in a fundamentally wrong place. Which this isn't: the OS is probably the only right place for access permissions.
An obvious solution would be education. Teach people how to use docker mounts right. How to use chroot. How Linux' chmod and chown work. Or provide modern and usable alternatives to those.
Your point about OS caring about this stuff is solid, but saying a solution is education seems a little bit naive. How are you going to teach people? Or who is going to do that? If node runtime makes its use safer by implementing this, that helps a lot of people. To say people need to learn themselves helps noone.