It's a lot more of a hassle, though, to ask users to keep an extracted directory sitting around which Chrome basically symbolically links to, than to just download a .crx, drop it on the extensions window, and then delete that .crx.

Even I still get confused sometimes, as a chrome-app developer, when I move a project folder and Chrome suddenly can't find my extension. It goes against how we think of "deploying to test" in any other development workflow.

Right, so thats why .exe installers for extensions will now be popping up, which is not exactly better security-wise.