The BODY multipliers for the hit locations sometimes make it easier to kill someone with small KAs. A heavy pistol is about 2d6 RKA, doing an average of 7 body. Two average hits leave the 14 BODY character dying. Now, shoot him in the head. ONE average hit leaves him dying.
I don't find that at all unrealistic.
Now, as for the "doubling," I see no reason to assume that it applies to anything but lifting. There's nothing to imply that the game mechanics of damage, BODY, STUN, or defenses are anything but linear.
The "muzzle energy" example doesn't hold up to a quick glance at the weapons chart in Hero 5th, or a little knowledge of firearms. A .50 BMG is listed as a 2d6+1 RKA, which is about the same damage as a very heavy pistol, which is too anemic for the .50 BMG. A .50 BMG hit to the body or head should be, on average, overkill -- about 3.5d6* RKA if the average person has 10 BODY. The .50 BMG, fired from the typical weapon made to fire that round, also has many times more energy than any pistol round, including the .50 AE that's listed as doing the same damage. If you don't understand why the idea of both weapons doing the same damage or having the same energy is a joke, find someone who has handled both a .50 BMG and a .50 AE round (or better yet, someone who has fired both) and ask them to explain it.
* "Three and a half D6." 3 1/2d6 looks like gibberish.