The main website seems to be down for Mr. Goodin's blog, but here is a link to an article on Scribd.
The Why of Bunkai: A Guide For Beginners
The article is VERY good at understanding how karate started to change in its approach to bunkai with the use of labels. Originally, a student would have learned the motions of the kata and its various uses. Not all of the motions in the kata are blocks, but when you put labels on the motion, it then locks that motion into place, so to speak. Then you have all of the "tier one" applications that were not intended as a simple block/punch technique and get VERY disfunctional applications based on the tier 1 idea. For example, you are doing to separate blocks to two different attackers in multiple directions.
Now we further the "telephone" game with karate's transmission. Funakoshi admits that he made further changes to the original kata he learned when he brought it to Japan. Funakoshi did not like free sparring that the Japanese students liked. The kumite that was introduced was based on the sport of kendo and it's distancing and relied heavily on the 'ippon kumite' idea. This is why none of the applications from their kata/kumite make sense and the sparring looks nothing like the moves from the kata. The Shuri kata that Funakoshi learned was based on civilian self-defense and the moves and applications were based on very close quarters and responses to a variety of those common attacks (McCarthy coined the terms Habitual Acts of Violence).
So, now this changed karate is transmitted to Korea and the applications are all taught as block/punch/kick. TKD used to be heavy on the kihon and hitting hard to break whatever you touched. There wasn't much sophistication to what was taught in the early TKD days, but it was very brutal and effective. "A Killing Art" is a very good read about some of the history of TKD and its formation. As TKD evolved, they tried to remove more of the Japanese influence out of it and removed the Japanese katas and replaced them with katas of their own. Sticking with the same idea of block/punch/kick, the sequences were moved around and based on aesthetics and not a deep underlying combat strategy. This is also when the more acrobatic kicks started to be added in to TKD to emphasize an older Korean art/game and the art started to become its own style very different from its parent art of Shotokan.
As you, and many others have seemed to notice. The kata in TKD help with body mechanics, fluidity etc. but, without reverse engineering from the older Okinawan katas (Mainly Shorin-Ryu) and trying to find sequences that look very similar and finding those applications, there IS a large void in many TKD schools. But, there are many out there that do fill the void. KKW TKD is mainly concerned with its own sport and its main focus is on the sport of TKD, just like any martial art there are exceptions to this, but by and large you won't find "old school" self-defense and applications taught and it is not taught through the vehicle of their forms.