I assume that one major difference is that the web apps are treated as separate applications from the main browser, so they get put in their own icon on the Uni

I assume that one major difference is that the web apps are treated as separate applications from the main browser, so they get put in their own icon on the Unity side bar, which gives them their own keyboard shortcuts and the ability to pull up just the windows related to a single webapp. For example, maybe Super+5 would be the shortcut to either activate your existing Twitter webapp window or open it if it isn't already running, regardless of whether your regular browser happens to be running or not at the time. If you just had multiple browser windows open, they would all be together on the Firefox (or Chrome) icon and it would be difficult to distinguish them. The important part is that the name of the executable associated with a window (i.e. firefox/chrome) is no longer synonymous with the identity of the application running in it (i.e. Twitter, Gmail, Facebook, etc.).