It is possible to create a stack that hasn't been specified in a region file when a template matches the supplied stack name.
For instance, let's say one has templates/FooStack.json without a reference or use of FooStack inside their region file. If one were to run stacker update FooStack stacker will create the FooStack in the default region. I think it's safe to assume this would only occur when the template supplies all the default parameters or has none at all.
I'd expect stacker to check for a reference to the stack in the region file before proceeding. A message letting the user know they need to define a stack in a region would resolve this nicely.