The difference between web apps and the former gaia apps are that gaia apps have been Firefox OS packaged apps.
Packaged apps are apps build with web technologies, but acessing gecko speciffic privileged and certified APIs. They could never run on the web since those APIs do not exsist on the web.
Chrome packages are bundles of html / css / js which are part of the system UI. As you can see they are also writen with web technologies like web apps but are A stored on the device and B executed with chrome privileges.
Chrome privileges give them the ability to access Gecko internal APIs which are not accessible from the web.
Webapps are applications served from the web, using web APIs.