None of the Freedoms below prevents you from overflying or landing per se; what countries want to do is ensure they know who is going over their airspace beforehand, so they require an application. To compare, as a freedom you're allowed to drive a car, provided you pass a test and get a licence.
Much of the permit process is to do with ensuring operators pay - or have paid - their bills for airspace usage, and a few countries require copies of aircraft docs to ensure airworthiness etc, as well as details of load (DG, surveillance equipment, pax names sometimes). Afghanistan, for example, raises millions of dollars for being in the right place geographically between Europe and Far East.