As I see it the advantage of a seacock versus the flange and a ball valve is one less joint that might leak. Another consideration is that the entire seacock (except for plating on the bronze ball in the valve part is the same metal so there will be minimal electrolysis issues. In contrast, it is likely that the flange and the ball valve could be made from different grades of bronze (the ball valves may even be brass if you cheap out), which increases risk of electrolysis.
In the unlikely event that the seacock fails you are pretty much going to have to haul out to do the replacement. However if the seacock is bolted to a backing plate and not through bolted, you could replace it as easily as you could a ball valve. For example, when I installed my seacocks on my glass boat, I put in fiberglass backing plates which were drilled and tapped for the seacock mounting bolts. The thru-hull has its nut on it, so I can, in theory, remove my seacocks by unbolting from the backing plate and then unscrewing them from the thru-hulls. If they are thru bolted you will have to haul to replace them.