I have no issue with what you say both, it is logical and in any case, it is always easy to accept the rationalization or assumption made by Steve...
Just, that's something I would have liked to see, this added logistic... but I don't see this happening any time soon, Steve is probably not interested in adding yet another extra layer of micro-management, which, to be honest would have to be handled mostly by the civilian sector. I'll rest my case!
Perhaps what bothers me more is that I feel there should be decent, even significant, civilian traffic at all time, from home world to colonies and between colonies when properly developed. But perhaps it is what will happen if trade goods get exchanged correctly between them?
It also means we must have some tools to interdict solar systems to civilian ships, when there are hostiles. I think it is in. What is not though is a convoy system, as set by the allies in WW2. Civilian can travel, but under escort. Or Civilian can travels, but only in groups.
That would be great to see a bunch of merchant ships escorted by a few second-rate escort destroyers