I've always created the dedicated server first, it will run without a war room connection.

or just with a cmd line , here is an example

 -ip=11.22.33.44 -port=2302 "-config=C:\arma\TADST\GhostB\TADST_config.cfg"  "-cfg=C:\arma\TADST\GhostB\TADST_basic.cfg" "-bepath=C:\arma\battleye" "-servermod=@aliveserver;" "-profiles=C:\arma\TADST\GhostB"  -noTexHeaders -name=GhostB_Pub -enableHT -filePatching -LoadMissionToMemory "-mod=;"

What I use, is https://armaremoteadmin.com/ mostly for the steam mod updating.
You can select mods with both armaremoteadmin and tadst but you need to add the server mods.

In TADST you need to add -server mod=@aliveserver; to the extra parameters

or add -servermod=@aliveserver; to your parameters.

The code line of the support module I believe

Just get the script version and copy the vcom folder to the mission, (I use the their github, I think its more up to date, maybe?)

and add the following to your init.sqf

////////////////////////////////////////////////////////////////////////////////
// VCOM AI 																																		//
// https://github.com/genesis92x/VcomAI-3.0      			  											//
////////////////////////////////////////////////////////////////////////////////

//Exec Vcom AI function
_vcom = [] execVM "Vcom\VcomInit.sqf";
waitUntil {scriptDone _vcom};

//Globally disable VCOM_AI for Air units including Combat Support and Logistics. 
[{{Driver _x setvariable ["NOAI",true];} foreach (vehicles select {_x isKindOf 'air'});}, 1, []] call CBA_fnc_addPerFrameHandler;

and the following in to your description.ext

////////////////////////////////////////////////////////////////////////////////
// CfgFunctions																																//
////////////////////////////////////////////////////////////////////////////////
class CfgFunctions 
{
	#include "Vcom\cfgFunctions.hpp"
};
////////////////////////////////////////////////////////////////////////////////
// Extended_PreInit_EventHandlers																							//
////////////////////////////////////////////////////////////////////////////////
class Extended_PreInit_EventHandlers {
	VCM_CBASettings = call compile preprocessFileLineNumbers "Vcom\Functions\VCM_CBASettings.sqf";
};
////////////////////////////////////////////////////////////////////////////////
// CfgRemoteExec																															//
////////////////////////////////////////////////////////////////////////////////
class CfgRemoteExec
{
	// List of script functions allowed to be sent from client via remoteExec
	class Functions
	{
		mode = 2;
		jip = 1;		
		
		class vcm_serverask { allowedTargets = 0;jip = 1; };
		class VCM_PublicScript { allowedTargets = 0;jip = 1; };
		class BIS_fnc_debugConsoleExec { allowedTargets = 0;jip = 1; };
		class SpawnScript { allowedTargets = 0;jip = 1; };
		class enableSimulationGlobal { allowedTargets = 0;jip = 1; };
		class VCM_fnc_KnowAbout { allowedTargets = 0;jip = 1; };
		
	};
	
	
};

thanks

Is it possible to alter force size for military and civilian placement during the missions, or a way to delay the mission being initialized till the ready room and adjust it there?

Sorry, typo, I meant the Virtual AI System not commander

You are placing empty aircraft with no crew, synced to the Military AI Commander, and you have an available force pool?

I believe you need to set Resupply to yes also

http://alivemod.com/wiki/index.php/Military_Air_Component_Commander

I always put a marker around any location players will be operating out of, airfield, base, and so forth, then blacklist it.