Ted, I can't give you the "why" (that would be an Alton Brown question) but yes cooking does change flavor. Think if you put all the ingredients for chili in a pot and didn't cook it. And then how it tastes after an hour of cooking...or a few hours of cooking. Even the next day.
And I've read that the lycopene is more available after cooking vs raw...so lots of chemistry stuff going on there.