[idonthaveaname]

The points apply equally to those things you call "applications" as they do to those things you call "sites". They're essentially the same thing. They're all functionality delivered over web technologies and for that reason, the OP's points still hold. In the case of a "web site" the functionality is "displaying content".

An "application" can be built using progressive enhancement. The OP even describes ways to approach this. There were applications before there were AJAX or Angular. Their experiences leave a little to be desired, sure, but they were certainly usable. A basis in simpler, server-centric interaction with enhanced, client-side experience jazz is still more in-keeping with "how the web was made", and with how it is consumed.