Sure a scenario does not have that much configuration. But not all values are fixed either. At the moment you can change nothing but the game speed. Which population limit you want is more a question of hardware possibilities than map design, and depends from the number of players. I do not want to change the options defined in the map with atlas editor but those not defined. Not all scenarios define every value.
For those values that are not fix in the scenario, the last values used in a skirmish map on the host are used. Including team options, and these can be everything, including things that are not suitable for the scenario. For my usage I have found out how to deal with a situation like this. For the game I think: Values from the map, defined by the creator of the scenario should be fix, all other changeable, and not last values on the host used.