Q: Is it possible to modify the system configuration in order to customize it?

A: Yes, it's possible. In order to modify and manage all the functionalities and the behaviours of the mobile device the administrator can use both the system utilities (if present) or modifying some configuration files or scripts (for example for disable the desktop's startup, disable system's functionalities, remove unused utilities, launch automatically user's applications at the system startup, etc.).
The first script executed during the system's startup is the file /etc/inittab: starting from this file the administrator will can follow the boot sequence of the mobile device, and will be possible to change files and scripts in order to modify the Nylux behaviour. Possibly, if the administrator will decide a configuration to apply to much than a single Nylux, it will be possible to package all the settings in a single tgz file (that will contains all the files and scripts modified), in order to install easily the same configuration package on other mobile devices.