It's embedded in the ground in the E3 and PCgamer builds in the same spot. As we all know from build 96, the terrain height was lowered at some point. For whatever reason, the padlock's position wasn't altered to account for it. So while it's probably still related to the nearby shed, it seems it was never intended to be attached to it. (and yes, it's the black rectangle in the first photo.)
Naturally, IJ took a much different design direction as development progressed. It went from a dense beautiful jungle, to a dense rocky sad forest with fewer trees and lots of gorges.
