On the subject of using massive commercial shipyards to build ships without engines instead of stations using industry:
The net advantage of using shipyards over industry are, I will propose, overrated. The advantages are real - and I will provide some (introductory) numbers to show this. The disadvantages are also real. Aurora, in short, is more finely balanced in this regard than it is given credit for.
Example:
You want to build a suite of stations, each to be towed between jobs. For one of these jobs, mining, we design two orbital mining stations, each with 100 modules. The armorless (station) one costs ~14,940 BP, the armored (ship) costs ~15,480 (doesn't vary very much with tech).
We use build rate 25, shipyard rate 1300 as examples, but these comments apply for any equivalent tech levels.
The ship is built with a shipyard. It requires a shipyard of ~516k size, which at 30% shipyard time/cost savings, needs 2400 + (16.8 per k of shipyard size * (516k-10k)), 2400+8652 = 11,052 minerals to make and 12.9 million workers to man (regardless of tech). Assuming no components are made elsewhere, the shipyard (at 1300 build speed and no bonuses) takes approximately ~15,480 / 7450 = ~2.08 years to build. I ignore retooling costs here, which may be nothing ... or considerable.
The station is built using industry. Let's say we desire to match the speed of the shipyard. At equal tech, we'll need ~7450 build speed / (25 build per factory +no bonuses) = ~298 factories. Adjust for the only slightly different cost of the two vessels, and you end up with ~290 factories. These require 34,800 minerals to make and 14.5 million workers to man.
While the number of workers isn't vastly greater, a) the mineral costs and build time of factories are a LOT higher. This is true even at the beginning of the game - and the difference becomes even more stark as Shipyard Operations tech advances!
But factories are more flexible.
Say you want to change the model of vessel you produce (say, you now have a bigger empire and so want bigger orbital miners). Factories can do this instantly; shipyards require time and resources.
Devote scarce manpower to factories instead of super-shipyards and you get options you did not have before. You want to build one type of station quickly? A planet full of factories can crank them out more rapidly ... than anything short of a shipyard that chews up almost a planet's worth of manpower all by itself. The shipyard gears up far more quickly and efficiently, but at the expense of most other possible needs for the manpower.
You have a military crisis, or just want to turn new tech into a fleet in training more quickly? Use factories to make components for your military shipyards. You want to build more mines, more financial centres, more research centres, etc.? If you've put the manpower into additional factories, rather than super-shipyards, you can do all of this faster.
Aurora, as already stated by several posters in this thread, asks the player to continuously balance multiple desires and needs - manpower, mineral, and wealth growth; technological progression; military defence. Putting more manpower into factories - as opposed to super-shipyards - enables you to act more flexibly to match emerging needs and face down sudden crises.
None of this means you should not build ANY super-shipyards! I use them all the time. I've even got tugs to swap them in and out to use manpower more flexibly. Yet my main reliance will continue to be ... more factories.