When building something new, I'm pretty sure that an Mk II engineer builds 50% faster and consumes 50% more resources. When repairing something, like ships, damaged turrets, or even a golem, you pay a fixed price per engineer, but still repair faster with higher engineering rate, so the engineer with the higher rate will save you both time and resources.
Using say, experimental engineers (engineering rate 5) to construct ships or buildings will cause a huge drain on your resources, but you should see the suckers repair things, its practically free, stick 5 of those guys on a golem and repair it in 6 minutes flat with incredibly low cost. I <3 experimental engineers.
Still, the primary role of engineers is to assist in construction of ships and structures (MRS takes the role of repairing), so in that ragard there is no real advantage to using higher tier engineers. You pay the same amount to build ships, and you pay roughly the same maintenance (energy) for that engineering power. Technically Mk III are cloaked but they become visible when repairing/building so I'm not sure how much of an advantage that is. Perhaps if they just all had the same energy cost (4000), it would be more efficient to use the higher rank engineers over lower ones for all uses.
