Does it make a difference, other then achevments, whether you knock out a person or ignore them? I mean in the end game or with how the environment changes?

I do not mean with acheivments.

Basicly are they the same thing?

they are the same, cept avoidance means theirs no chance of bodies being discovered.

I'd rather avoid any confrontation during a stealth playthrough. One, there's a chance the body will be found. Two, you have to find good places for the bodies so rats can't get to them.

Avoiding is usually best, but if there are guards that are restricting your movement freedom alot, its way better to KO to get that piece of mind exploring safely. Particular in non-linear quest areas where you have to backtrack alot.

I personally try to loot and avoid as best I can but sometimes I do knock out some guards that may be a trouble later on. Nothing too problematic though.

My methodology.

http://imageshack.us/a/img132/7996/28244353.jpg

Mine too. Often a lot more difficult than just avoiding them, especially in this game.