For those that need to silence notifications but keep ringer volume up at night I found a program that works for me. I don't really know why it works since google linked the two volumes I can only say I have tested it and it works.
I use NightStand BOLD Available in Android Market. I use my Galaxy Nexus as a bed side alarm and if you select "Notifications Muted" at the bottom it truly does mute notifications but incoming call will still ring. The alarm also still rings.
I know this isn't a fix for everyone, but those that need to receive calls at night it seems to work on my Galaxy Nexus.
Hope this helps until google sees the error of their ways and corrects the problem.