How it works from my understand is this

The 3 towns are the main hubs.
Then each area has a destination from the main hub, which is the village / camp with the Crystal in, lets call the Area hub
Then from the Area hub there is two way single routes to and from Area hubs and Smaller camps


And the way it works is, you can only go via Main hub <> Area jub <> Smaller camps.

Which is the point of chocobo porter, providing a cheaper alternatively to travel which cost less but takes more time.
And you get the enjoy the scenary (like anyone care)