There aren't that many people who order an appetizer, an entree, and a dessert -- appetizers especially would generally be split among the table, as opposed to each person getting their own. If they are smaller appetizers to be sized as an individual portion, then the cost calculus shifts.
The other issue, as I mentioned, is the selection. It's not like you can pick from everything they normally offer on the menu. At the Edison, the prix fixe price is $65, and the most expensive meal you can put together from their options based on the standard menu price is $71. So you'd be saving $6 at most, but if you end up full after the appetizer and entree and don't want a dessert, well... you're getting it anyways. You don't have the option to just not order a dessert and save more money than if you'd gone with the prix fixe.
You could also put together a three course meal from their options that's actually $9 more prix fixe than it would be if you just ordered a la carte from the standard menu.
That doesn't mean it's automatically bad, but you really have to think about what you're getting from their options to make sure you're not actually paying more than you would have otherwise, even if you do want all three courses.