I do cargo groups of 5 freighters with 5 cargo holds each. This means each freighter can carry 1 mine or factory, and they're still cheap and easy to produce.
Once I have a planet that I want to "seed" with industry, I'll set up one round-trip of orders from my homeworld to the new colony, then hit Repeat with a factor of 19 keyed in. Voila. Continuous shipping of 100 mines, factories, whatever. Having multiple groups allows me to ship multiple kinds of stuff simultaneously.
True, it ain't fast. Currently, I have a set of cargo groups seeding the world Corinth (36 Ophiuchi B-III), to act as a new sector capital and administrative hub for the Trinity system (36 Oph is a hellacious trinary system with no less than six potentially habitable worlds and hundreds of mining opportunities). Total aggregate time for a cargo group to finish is about 6.5 years, because it's roughly 130 days travel time between the two. Though I think that could be fixed with the development of megafreighters with 25 cargo holds each (so that each is equivalent to one cargo group). A group of five of those would only need to make four trips, as opposed to the twenty trips it currently takes. As the travel distance increases, economy of scale becomes more and more efficient.
I've only recently started playing around with the use of civilian orders, but I like it. I have a LOT of civvie freighters floating around, so once I set up some contracts, I actually started to see decent movement of facilities. Nowhere as fast as if I directly moved them myself of course, but that stands to reason. It'd be nice if you could prioritize contracts by awarding subsidies or something. I have money out the wazoo, I'd be willing to spend generously to harness the civilian sector.