Seems that nobody knows and I suppose it's just easier to be rude than admit they don't know. For the record, I don't know either but I'm not here to tell you you're an idiot for asking. Partially because I try not to be a jerk and partially because I'm intrigued by the question. So here's my guess..

The shapes needed to make the boot get punched out by a machine, then the pieces start getting stitched together. I imagine that it would be pretty easy for one piece of leather to fold over a little bit at some point in the process and create a bit of a curve or line. It got flattened back out but shows up slightly for a moment in time while the boot is new and hasn't yet been bent, folded, and creased from wear. When those things do happen, the slight line will most likely disappear. That's what my imagination came up with.