I think the disadvantages are overstated. There where a few bad designs to start with and if you where an early adopter and backed the wrong standard getting parts could be very difficult. Now there are a few more popular standards and the bad designs where the bearings where pressed directly into the frame have mostly gone there are not many disadvantages.
The only disadvantage I can see to an internal headset is that they are not as comman as standard ones so parts are less available and there is less choice. An internal head set is pretty much a standard headset that fits in a larger diameter headtube so both the cup and bearing can fit inside the headtube.

I'd take that king article with a grain of salt, if all headsets went internal they would sell less. Same reason why phil hubs are a lot more popular than their bbs, people like to show off their expensive componants not hide them inside the frame.