I don't bother building my own freighter fleet in fact. I rarely use my own colony ships and freighters.
Ever since I found the civilians will honour contracts to transport infrastructure to empty colonies, it was a simple matter to colonize with zero government ships.
In fact, I only use government transport for research labs, critical infrastructure, and moving minerals. Colonists... well, leave that to the civvies. I have just a few on repeat to build up population centers away from the homeworld.
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I think building a "blooming civilian sector" is a matter of designing low cost budget ships. The huge 200kton ship is expensive, and the money the civ lines build up to save for the ship could have been in use as a few low cost ships.
During which time, the less efficient low cost ships have long paid for themselves before the huge 200kton ship even gets built.
Like I learnt the hard way in Star Ruler, it's all about economic doubling time. In a long term game like Aurora, you want your doubling time as small as possible, even if you have to start tiny.