Okay, here's how I currently understand repair to work. (Patch 5.050)
Construction cost is as listed in the ship description.
Repair Cost is 25% as listed, including Repair Time being 25% also.
The repair time is why repair is currently destroying economies.
Because repair time is also 25%, while repair is underway the costs per second are exactly the same during construction as during repair.
Except the rates are not the same on engineers, a Mark I engineer has Construction Rate 1, Repair Rate 6 so a Mark I engineer consumes six times more resources per second when repairing then when building the exact same unit.
Only showing metal to keep things simple but crystal works the same way.
Assuming an engineer could build a Light Starship without requiring a starship constructor:
Mark I Engineer building a light starship: 40,000 Metal Total over 05:34 for 120 metal/second. (Construction rate 1)
Mark I engineer repairing a light starship from 0 to 100% health: 10,000 Metal Total over 14 seconds for 714 metal per second (Repair Rate 6)
This just gets more extreme with higher Mark engineers. A mark III engineer at repair rate 12 would be:
Mark III Engineer building a light starship: 40,000 Metal Total over 01:51 for 360 metal/second. (Construction rate 3)
Mark III engineer repairing a light starship from 0 to 100% health: 10,000 Metal Total over 7 seconds for 1,428 metal per second (Repair Rate 12)
Effectively, the Repair Rate of a unit is the multiplier for how much more expensive things are to repair (both absolutely and per second) so the Mark I engineer consumes six time more resources to repair and the Mark III engineer consumes twelve times more resources to repair now.
A single Mark III engineer repairing an Armored golem now costs 8,333 metal and crystal per second. Let's not even talk about a swarm of engineers now.
D.