I have been told that the reason for cooking the garlic/onion first is to "layer" the flavors. I have also been told that onions will not brown if you add them to the meat raw.
So with all the urban myths I've been told I decided to put them through a scientific test.
I took a simple recipe for chili and tried four different methods to see if the appearance or the flavor was different.
1) cook the onions and garlic. Cook the meat. Add the meat, onions and garlic together. After simmering, add all other ingredients.
2) cook the meat then add the garlic and the onions to the meat. After simmering, add all other ingredients.
3) cook the onions and the garlic. Add the meat. Simmer. Add all other ingredients.
4) cook the onions, garlic, meat together. Simmer. Add all other ingredients.
In all cases the flavor was the same and no one could guess the difference. The one thing I did notice was that when you cook the meat and the onion/garlic separate they brown differently.
I guess there might be those people who have "super taste buds" and can pick up on the subtle differences in flavors but for the common person no one will notice because you are adding so many different flavors. Besides, many people I have talked to put cheese or sour cream on their chili which is, as far as I'm concerned, is overkill.