Assuming this image I found online is of 4680s, there’s quite a bit of wasted space: https://www.teslarati.com/wp-content/uploads/2021/01/tesla-4...
You can see that the cooling channels in the Tesla pack are these hollow undulating aluminum shapes. Can imagine they're not very cheap. Also the Tesla packs are filled with some kind of bonding foam, making repairs near impossible.
Is that maybe to reduce the spread of fire? I know Tesla put a lot of work into that. Others too, I hope.
They don’t bother with smaller secondary batteries because the extra manufacturing cost and operational complexity isn’t worth it for a 5%-10% bump in volumetric energy density.
You could probably ship them staggered, but I’m betting they are at a weight limit anyway so making them more dense doesn’t save you anything.