A fountain pen is, in essence, two tubes that screw together. The complication is that a pen kit has to allow space for the turner to cover those tubes, and for components to be pressed into them too. A commercial pen or a custom pen has no need for parts to be pressed in, so that's at least a few parts of a millimetre saved, and the bit you see, (what would otherwise be a blank surrounding a tube), IS the tube, so that's a few more parts of a millimetre saved. The necessary difference in size is what gives rise to the step.
As for a thread at the end of the barrel to post the cap, I agree they mostly look odd and I'm not a great fan of them. However, many tuners won't buy a kit if it's not postable, and many won't buy one if it does have a posting thread. It would be ideal to be able to post the cap simply by pushing it onto the blunt end of the barrel, but unless you give specific instructions to the turner about the exact size he or she is allowed to turn his blank, it won't work - those that like a fat curve on their pens will end up disappointed, and any deviation whatsoever from a strict tolerance would result in failure. It could be done by having a plain, non-threaded finial onto which the cap can be posted, but that would look just as bad as a threaded finial, and there would be a step at that end too, just as there is with a threaded finial, and just as there is with the cap thread at the pointy end.