Basically, no, it seems the module-defined battle size will override the player's settings. That said, it is perfectly possible for the module to take player-defined setting as a base and just scale it up or down as befits the currently selected map/scenario - so on a specific map all battles would always use 125% of the battle-size set by the player for his own machine. But it depends on developers - they could be lazy and just ignore the player's settings.