Do you think this is intuitive behavior ...? I'm concerned that this behavior deserves an explanation somewhere.

No, it's not intuitive; however, this is pretty much the way references work in any computer language. Maybe see reference, perlref, perlreftut. Perhaps also take a look at the Monastery Tutorials articles in References, and maybe also at Coping with Scoping and other articles in Variables and Scoping.

(And yes, you need to adjust your thinking :) (Update: And yes, references and aliasing have bitten me, too — many times, many, many times...)