There's no expectation that sites ought to work perfectly with 500% zoom, even though a browser supports that as a zoom value. The same way there's no expectation they work with a horizontal viewport size of 50px. Because they're the same thing, and when you push any design too far it breaks. That's just reality.

And with page overlays, text zoom isn't necessarily going to fix anything. Sometimes the button to dismiss is at the bottom, and the larger text will just push that off-screen downwards. (I do agree that pop-ups/overlays designed for a screen larger than yours are a problem, but that's often less about zoom than just assuming small/short phone screens no longer exist.)