This is only theory, but it must be a configuration file (CFG or INI) to load the user's settings when launching the Exosphere (the official Atmosphere GUI, call it FuseeBoot: P), and it is hosted in the MicroSD. Since I do not even have a MicroSd, I'm not sure if I create this file when I run Exosphère. So I do not really know that it can contain this file and how to configure it, but it sure is customizable in case there is the option to activate or deactivate options that are in Exosphere. It is not yet available to the public, but it can be created or modified if someone has already obtained it. As Exosphere does not find that file it creates a temporary factory configuration. Exosphere also asks for the payload mentioned "stage2.bin" and looks for some "initiator". Perhaps these two files contain the routes and keys necessary to run Atmosphere.
As I said, they are not available to the public, they are not identified in the repository until suddenly the official launch of Atmosphere.