The recipe is for the stove top. If I want to do it in the crockpot, I make it up to the point of adding the cocoa powder, excluding the canned tomatoes and water, and stick it in the fridge overnight. Early in the morning I dump it cold into the crock pot and add the tomatoes and water. Then I drain and rinse the beans, leaving them out to sort of dry off in the strainer. About half way through the day I add the beans and cilantro.
I usually use a good chicken stock instead of water and use less than half the amount suggested making for the crockpot. Unlike the stove top, it doesn't boil away quickly. In fact, I don't use the full amount when I make it on the stove top either. I like a thicker chili.
I use more than a "pinch" of cinnamon and am generous with the other spices as well.
I use yellow onions all the time. I don't think the red affects the flavor, it's just a color thing.
Use gloves when you cut up the chipotle pepper. Even though it's canned, it packs a burning wallop by itself. It's a wonderful flavor in the chili, but there's a reason the recipe only calls for 1/2 a pepper that's the size of your thumb. BTW, don't worry, this isn't a "hot" or "spicy" chili. It's just flavorful.
The sour cream and grated chocolate change the whole flavor. They really are a must. My kids are mild chocolate only, but on this, they eat the dark chocolate and in fact, have a good time grating it after they serve up their bowl.