I've actually used static bundles (including css/etc) for a lot of internal applications, both at home and at work.
Basically anywhere where reducing difficulty of deployment and asset management outweighs the valid concerns you pointed out. It's really, really handy in my view.
Of course, I've got no plans or desire to run some production documentation site on this. Yet, that problem domain is vastly different than internal tooling, OSS apps, etc.
Just think of a note web app you write. Do you want your users to have to manage css/template/image bundles just to use your note app? Why not just make the binary work with zero configuration/management? Plus, if you wanted - you can of course support both, allowing the user to override css files if they so desire, without having to recompile the binary/etc.