Yeah, I have went both ways on the sauce recently. The first pizzas I made were with an uncooked sauce from fresh Roma tomatoes I got at Whole Foods, and I just found that they never reached the level of flavor that I wanted, and I even made a deep dish with the uncooked sauce and it just didn't really please my palette even though it cooks for a good bit longer than my usual pie. I consider myself to have a pretty developed palette for a college guy too.
But yeah, I like the flavors that the red pepper adds when you sauté it with the onions and garlic, it damn near burns your eyes if you stand over the pan. The roasty flavors you get just can't be had in an uncooked sauce, I guess because no maillard reaction occurs really unless the sauce gets hit with a broiler directly. But that is just my opinion, and it isn't that I dislike uncooked tomatoes. My favorite sandwich is a plain tomato and mayonnaise with salt and pepper, and I love them fresh on a good caprese salad.
And as far as Alton goes, I really do like his show a lot. I think that he puts a good amount of effort into what he does and is the only cook on the entirety of Food Network that is worth watching. The rest of them are nothing more than actors if you ask me. There are things that I found I disagree with, like recently him not balling his pizza dough before he bulk ferments it. But as far as his sauce goes, I like it cooked as well and reduced to a fairly thick consistency. He does do fresh "sauce" on the grilled pizza episode though, and if one uses a WFO oven I think it would be a travesty to employ a thick cooked sauce. But for my American and NY style pies I've been doing recently I enjoy it cooked. If I crack open my D.O.P. tomatoes I recently found though I may feel differently, but I am saving those for a special day.