I'm going to speculate that these little 'dents' were used as master positioning markers. If so, were they created to guide the panel-stamping/forming process? Or, instead, were they used to guide and/or check the positioning of the stampings in their jig prior to welding? The latter seems more likely.
One wonders, then, what prompted the change in orientation of the dent in the rear floor deck stamping after less than 100 units had been assembled. Perhaps the performance of the assembly jig in its original design iteration wasn't delivering adequate results, making this small-but-important change necessary before the production process ramped up to full speed.