I feel like the End's boss is good because you can just say "fuck this!" and chase him around the map with your thermal goggles on and just spam the cig spray. Then on a second playthrough you can choose any of the other billion methods to deal with him. It puts a lot of the options you have throughout the game into slightly clearer view.
Like for instance I thought the Fury was just a skill challenge but on my second playthrough I mostly stealthed through it by moving slowly until near the end when I just put on the fire camo and just punched him in his face a bunch. Also if you manage to knife him with the survival knife you can cut his suit and certain items become more effective and oh man is it easy to ramble on about all the stuff you can do in 3.
As far as cqc'ing the Boss I had that same issue during my first playthrough but during my second playthrough I got a little closer to understanding how to do it. Unfortunately I still couldn't manage to understand how so I ended up finishing the fight with the same technique you used. That being said I think that if I kept replaying that fight again and again I might just learn it more on instinct then comprehension.