There are no advantages or disadvantages of one over the other... They are intended for two entirely different styles of shooting.
The 6 o'clock style is used with bullseye shooting, and allows you to properly see what is generally a very small bullseye at a great distance. The POA approach (where the front sight typically covers what you want to hit) is used in combat shooting when you're trying to hit something nearer, quickly.
I tend to use a combination of both: I have my sights adjusted so that I look across the top of the sights, with the dots aligned (or the Glock-style box/front sight or SIG dot/bar aligned). For close-in shooting, this approach doesn't make much of a difference, and if I'm shooting the same gun in at bullseye-type targets, at greater distances, it still works.
