SC2Mapster

On map initialization the Load Coop Mission action is run which in turn uses Load Allied Commanders Data. This then relies on several parameters for a decision tree to determine if the map is being played offline, arcade or in blizzard debug mode (lots of troll code). Eventually the CC_PlayerCommanderSet action is reached which does the actual determination of the selected commander. This has the default to Artanis, Raynor or Kerrigan troll code in it. This action is used at 5 points in the action tree to try and force players to use the defaults.

What determines if a player is a commander for non blizzard maps is the Preset Coop Players entry under the User Data data type. This is used by the Coop Preset Commander And Team action of the Load Coop Mission action. This determines if a player is considered for the Active Commander function (Commander Of Player does not work in non blizzard maps). The commander specific tech trees are done by the Player Commanders, Camapign Perk and Campaign Tech Unit entries under the User Data data type and mediated through the CC_ApplyTech trigger action definition.

As specific commanders cannot be set for non blizzard maps the CCX_PlayerCommander variable is used while the CU_GPInit action definition does the calldown bars at the top of the screen.

There is this demo map of mine where I have unlocked coop for easier customization.

https://www.sc2mapster.com/projects/the-assets-of-evil/files/2496461

The blizzard allied commanders mod is used for all coop maps. I was referring to it in my previous answer. The Load Coop Mission action requires a specific trigger to be set in it.

Another problematic part was the ally player function in that a lot of important stuff uses the old one.

Well As I said it uses the four actions under the CC_ApplyTech trigger action definition to hide the stuff. If you want to add stuff again then you need to wait until it is done else your modifications will be reset. Once you upgrade the level you need to refresh the perks. Look how the debug level up button does it.

I should have a new version of the template map ready by the end of the week. It always breaks when they add a new commander. Also the prophecy of zeratul is not designed for multiple players to select zeratul at once.

There were multiple things that needed alteration to unlock the commander player number. You need to expand the Human Players player group, under Load Allied Commanders Data you need to increase the number of banks preloaded for the number of commander players. The  CCC_MAXCOMMANDERS_PVE variable needs to be increased and all stuff that uses it needs to be duped and linked up. Make sure the user data under the data editor used by Coop Preset Commander And Team marks the right players as commanders. You also need to change everything that uses CC_PlayerAlly (Old) which is a big job.