This is clearly not 'all of userspace'. Autofs is an exception. As is /etc/mtab. The way I see it, automounting is a 'mount facility', as are namespaces. The two should be made to work together. Yes, mount(8) should probably be fixed one way or another as well due to /etc/mtab breakage. Why? Because it too is a mount facility.
There are a couple problems inherent with namespaces. Most of these are mount facilities that are broken such as mentioned above. They *should* be fixed to work nicely.
Other parts of userspace get confused with namespaces, eg: cron and atd. These programs clearly need infrastructure added that somehow allows for arbitrary namespace joining/saving. If you have suggestions for how we can solve this issue, please do let me know. I'm stumped :\ I'd be more than happy to discuss this with you.
One not-so-far fetched approach would be to associate cron/at jobs with automount configurations so that a namespace can be re-constructed at runtime.