I am willing to bet that if you made three versions of the exact same recipe, one all extract, one partial, one AG, you could taste a difference. Of course, it depends on the style of beer. Some beers have so many other flavors happening that they mask anything out of the ordinary. But the denser boil carmelizes the sugars, creating a darker beer and possibly a somewhat buttery underflavor, and it also does not allow the hop flavor or bitterness to be utilized as efficiently. Generally that is compensated for ina recipe by upping the quantity of hops somewhat. More math than I know how to do off the top of my head, but tables, conversion rubrics, and software all exist to help out.
You can carmelize with AG, but it has to either be done very intentionally, or you have to not be paying any attention to what you are doing. I just listened to Jamil's "Scottish Ales" podcast today, and he talks about intentional kettle carmelization during an All Grain brew. In order to do it, you run your first gallon or so of your run-off into the kettle on its own, boil it down to about 0.5 gallon, and this creates unfermentable, carmelized sugars. Then just add the rest of your batch and continue like usual.