I think what you are looking for is changing the settings of the NW_Sample_Battle.txt file. (or any of the other NW.txt files depending on which is used for the server startup).
In that file there are all the base settings for the NW server to run. For example this line
set_pass_admin YOURADMINPASS
sets the admin pass to whatever you type after it.
The settings that you are looking for are:
Spoiler
#adding all nations to both sides just to randomize all of them
#adding less nations will reduce the randomization set (used in set_randomize_factions command)
add_factions fac_britain fac_britain
add_factions fac_france fac_france
add_factions fac_prussia fac_prussia
add_factions fac_russia fac_russia
add_factions fac_austria fac_austria
set_randomize_factions 1
For the factions. The scene rotation is done in the following way:
Spoiler
set_map mp_arabian_village
add_map mp_arabian_village_morning
add_map mp_avignon_morning
add_map mp_beach
add_map mp_beach_morning
add_map mp_countryside_day
add_map mp_river_crossing
add_map mp_swamp
Where the set_map will be the one that starts first, and then it will just run the list of add_map in order.
For customs scenes, you can easily edit any of the standard maps into something custom, for example you can make mp_beach_day into a city surrounded by plains.
Note that all changes to the NW.txt file requires the server .exe instance to restart. So you wont be able to change the random factions on/off without restarting for example.
You can however use customized scripts to do that for you, you just need to know python to implement them
Same goes for the change of numbers for unit types in commander battle. Those ratios are fixed, so you need to customize your script file to change them. Luckily it's already put in that skirms/rifles/lights units get a few less soldiers than a line in commander battle.
The dropping and rising of the normal squad size is again doable with custom scripts to automate them. However you can just have good admin coverage to negate that problem, since the admins can just change the unit size accordingly.
Hope these help you
~ World