In botnix, all user flags have distinct privilages. No flag indirectly gives the permissions of another flag as in other bots, which makes it easier to securely compartmentalize privilages. Each flag may be assigned locally (to a channel) or globally (to a network or to all networks). The exception to this is the owner flag which if it is assigned locally, takes effect globally because of the far-reaching implications and effects of this privilage, in much the same way as the root account on UNIX systems.
The operator flag allows operator-style commands such as OP and DEOP which generally effect channels. Users with this flag are not able to permenantly effect the bot's state beyond channel-local actions such as setting sticky bans.
The master flag allows user manipulation of users below the master, for example users with the operator flag - a master may create operator users, delete operator users, or change their hosts and passwords. They can be classed as a form of 'department manager' allowing you to sub-lease your bot to channels if you wish.
The owner flag grants super-user privilages to restart or shut down the bot and manipulate the accounts of all other users in the userfile, however it does not indirectly grant operator privilages to OP and DEOP etc, these must be granted seperately.