I think you are completely misinterpreting the cause of the "Sneak Crit"....your weapon is not doing more damage (per se), your ability to surprise an enemy and land a better placed shot due to their unawareness is what is causing more damage. I get it's kind of "iffy" as a reasoning but do you not agree that you stand a better chance of causing more damage to any enemy if they don't see the attacking coming? It has nothing to do with any change to your actual weapon damage.
Now the idea that it ALWAYS lands additional damage is highly questionable and the chance should be effected by training (your perks and "skill") and the enemies current state of awareness (whether they have actually located you or not).
Certainly any "glitch" that allows you to sneak just before the hit lands and gain the extra damage is something that needs to be addressed, but that is simply an exploit in the system that can easily be avoided by a player. That particular glitch also sounds like it is also dependent on the AI detection range, not just the general sneak critical system.
I'm not convinced that the meter ONLY charges while you are in VATS....I certainly haven't seen anything that implies combat out of VATS can't charge the meter and / or there might be some Perk that determines how the meter charges as well as how fast (I think LUCK itself effect the charge rate in some way).