I'd say it's natural. Softer material eroded away leaving the depression. Some believe that nutting stones are actually hammers with the depression used for gripping. Battering evidence is common along the edges.
I have read about an artifact called a ‘Paint Pot’: a palm-sized, hand-held pigment mixer/mini-mortar used by NA artists.
Unless the bowl has obvious pecking marks, grinding lines and or (even better) pigment residue, it’s impossible to positively identify (as these are the identifying features).
Also, The ‘nutting stone’ identification of stones with multiple pecked indents about knuckle-deep in general is a de facto designation. We know that a variety of nuts were a major part of the NA diet and there had to be a way to de-shell the nuts en masse during the harvest.