I decided to test custom scenarioing with the commander to find anything interesting. These are my notes:
You can add Commanders to slots, in the territory you want them, while making custom scenarios...
...But you cannot cheat the game by giving you a Commander without giving your enemies one.
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I also tried giving Neutrals a commander. The game allows you to...
...But you can only assign it, not play it.
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As you saw from above pictures, I also tried to add multiple commanders to the same slot.
But once again, it's a no go. :(
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No loopholes this time around. Good job, Fizzer! But it sure as heck would be fun to play games with special rules without this binding.