Why do 16340 Li-ion batteries have low volumetric capacity?
Spiral wound cells may not make effective use of volume at the inside.  If you imagine starting to wind the same way and stopping at 16 or 18 mm, that extra volume is all usable but part of the core is not.

Similarly, the case and endcap losses are spread over a larger usable volume, so less signficant.

There may not currently be as much market pressure on this size either, which may mean both less optimization and less tendency to publish specs that are, (shall we say) "optimistic".