I believe the reason they used those bolts at the factory was for speed in assembly and less parts (no washers) to add. Other than that I see no advantage in using the factory style bolts.
Stainless bolts are great way to go. They look good and won't rust. Like miketyler said , be sure to use anti-seize on the threads. Stainless threads have a tendency to gull and can be a problem getting them apart if you put the nuts on dry.