This is an interesting question. It makes some sense when you consider the lack of visable infrastructure in SEIV. Population growth on colonies is too fast, and yet homeworld populations stop the moment they hit an arbitrary limit. Resources are shared throughout the empire by the simple act of building a space port in each system, no tranports required.
I have always taken the view that there are a number of smaller "non-military" vessels flitting about that are not shown in the game. Resource traders, space liners, private vessels. And the great rate in reproduction rates on colony worlds and arbitray limits on the homeworld can simply be ignored and considered as a function of this. Call it a low level background population movement. As opposed to the "state controlled" mass movement of populations via the colony ships and military transport craft.
This can also be used to explain the blockade of planets, as the stoppage of these vesels. And Abandoning populations can be thought of as simply finding passage by this other means to evacuate the planet.
Of course non of this justification is neccesary to play the game, but it helps me.
Geoschmo