Like normal Raspberry Pis running Raspbian. The config.txt file is the first thing the Raspberry Pi checks when it loads up off a PiNet based SD card.
The config.txt file can contain some key configuration/setup variables which can be used to set stuff like monitor resolution, overclocking etc.
A full list of the config.txt supported values can be found here.
Although a complex job to do in the background, PiNet allows for custom config.txt parameters to be appended to the default config.txt file then pushed out to all the Raspberry Pis.