I like the basic idea.
The problem with locking doors and the "stay indoors" command is the first is a binary thing - you can't forbid workerdwarves form going out your main gate whilst allowing soldierdwarves through without constant micromanagement - and the second is flaky at best as dwarves only pay attention to it once they are outside, when they realise "doh!" and run back inside. When they promptly turn around, go outside again...etc. It's definitely something that can be worked around but that doesn't make it good.
However I wouldn't use zones, I'd prefer some sort of furniture designation style mechanic.
For example, say the thing you need to designate your "emergency bunker" cavern is a big gong, which dwarves bash in time of emergencies / drunken parties.
You forge a *Massive Iron Gong* and place it in a cave you've carved out somewhere safe-ish. You can designate a room from the *Massive Iron Gong* in the same way you make dining rooms etc. Once done, you can add "bang gong" jobs to the gong, basht he gong once and it makes all (awake) dwarves come and stand in it's designated area, bash it again and it cancels the super-urgent "come here" job and the dwarves wander off to collect socks. Only active squad "station" and "patrol" orders override.
You could add all sortd to the potential randomness, dwarves ignoring it (eg if they're asleep, angry or really don't care about anything anymore), getting unhappy thoughts about being attacked (as the fortress is being attacked), needing food, drinks etc, but thats the basic idea that came when I read the OP.