This seems likely. I wonder if explaining it through the packaging, e.g. coloured stripe marked "stir space" and an explanation on the back saying don't worry you are only paying per gram of peanut butter...

Except that the larger packaging size is not totally free - makes shipping more expensive and less units per shelf space. Not sure by how much. I bet peanut butter margins aren’t great.

The top part of a plastic jar could be expandable/collapsible maybe. Thinking of something similar to the bendy bit in a plastic straw.

That (the designing & manufacturing, anyway) sounds like it would be even more expensive than simply shipping larger jars with empty space at the top.

I've seen some powdered dish detergent boxes do this.