Feif-
The difference is likely aptitude, and not method of study. Aptitude is a bad word these days, especially when it comes to academic pursuits, but I bet your uncle would remember whatever he learned b’iyyun as well as whatever he learned b’bekiyyus, while the folks Real Brisker mentions wouldn’t remember what Abbayye said to Rava 2 minutes by the time they started looking at the Maharsha.