What exactly are the "interrelated elements of the whole size thing"?
Ship size is one thing, and the only thing I'm really addressing with this "thesis". It ties in closely with cargo pod size, escape pod size and relative size of ships to each other. It also ties in with space station size. Planet size and relative distances between planet and star is a totally different "scale" issue and one that is up to people far more versed in astrophysics than I am to address.
Pentagonal sections are not great for stacking, I agree. They are, however, more stable than hexagons and less inclined to "roll" than hexagonal boxes. The best shape for stacking is still the cuboid though. Hexagonal stacking has its own problems, especially when it's possible that a hexagon stacked on top of two other hexagons will exert pressure and force in the diagonal rather than the vertical.
In an artificial gravity environment, that pressure would "force" the containers apart, and any bumping and jostling (like in combat) would eventually push them apart of there was any space to each side. Unless they're stacked vertically...
It makes me wonder what the actual designed method (the Galactic Standard, if you like) is for the storage and transportation of cargo in Tonne Canisters. They're obviously not designed for stacking. Are they designed to be laid on one long edge (as in the Adder plans) and opened like a chest? Are they designed to be transported and stored standing on the pentagonal face? How are the items inside kept from moving around inside the container? All this has an effect on how cargo bays are designed on the ships that are meant to be carrying them, and that has a big knock-on effect on the size of that cargo bay (especially when considering how to get the cargo pods in and out).
DaddyHoggy: I love the fact that your link goes to a page that shows a picture of a five-sided cargo container...

I have to be honest, until I started playing Oolite I was convinced that the container was six sided too - I think it came from the Amiga version.