In a two-player game, is it allowed to choose the flag symbol to bid 0 during war?
Michael Coe, the designer of Tiny Epic Kingdoms, responded to this question and said that it was allowed:


  Yes, a flag is a zero in 2 player games. If both choose zero, it's a tie and regular rules apply (tie goes to defender).


As Benjamin Cosman pointed out in his answer, a player may be forced to choose the flag if they have no resources available, so it would be very problematic for the flag to be disallowed in a two-player game.