This may seem like a "no-brainer" but it's not to me. I was looking over Challenge of Champions V from Dungeon 108. In "The Rules" the first line states: "All team members must show up in non-magic clothing; no armor is permitted."
What if some of the team members are warforged? It's not like they can just take off their armor/skin. What would you do to get around this beyond "That doesn't apply to warforged?"
Just remember the point of the Challenge of Champions - that the players have to rely almost entirely on their wits. Players should not have any undue advantage due to level or class. Disallowing spells, magic items, arms and armor turns PCs into "normal" people.
Keep that perspective in mind, and you should be able to turn any PC into a "normal" person, even if he is an armor-plated sentient construct. If I were you, maybe I'd invent an amulet that, when placed upon a subject, negates any effects of natural armor. Since such an item would be extremely valuable in the campaign (and outside Challenge of Champions), maybe it only works on a willing subject. The amulet was created by wizards that oversee the competition, and is "lent" to any warforged competitor. It can be an adventure hook too - the amulet is stolen at the end of the Challenge, and the wizards approach the players to recover it.
Or maybe the "testing grounds" are enchanted to remove natural armor effects during each competition. Perhaps warforged are required to be polymorphed into human form.
Just remember that if you remove the benefits of armor (such as an armor bonus), you also should remove any penalties (armor check penalty, weight, etc.).
You're taking it too literally. The races have their own balances :)
jh
Jeez guys, how about you just suck the creativity right out of the game?!? Make the fact that warforged are different part of the adventure. Why introduce a new race and create a new campaign world rich with realism and culture if you're just gonna throw out a "feh, treat all races the same".
P.S. Nice map, Mona!