The settings are saved in DVars, so you need to set these in the batch when launching your dedicated server.
gamemode_index 0-2 (Normal, One Room, Gun Game)
bossZombie 0-1
difficulty 0-1 (Original, Easy)
timedGameplay 0-1
startingRound 1, 5, 10, 15, 20 (only when timed gameplay is off)