All sailors' true ability in repair/restore contribute to the ship's overall repair rate, burn rate, and soft defense. This especially includes other support sailors, like engineers and planesmen, but also includes pilots, gunners, your BO, etc.

Only actual engineer sailors have their engineering true ability taken into consideration. This is because the number of engineers is part of the equation for how effective they are. (That also means that having 3 great engineers and 1 bad one is probably worse than just having the 3 great ones.)

The only other sailor whose engineer ability matters is a seaman, since he can provide an ability boost to every other sailor on the ship.

So having a 12/11/11 Rep/Res/Eng and a 12/11/8 Rep/Res/Eng are the same if that sailor is made a Rep or Res (eng ability doesn't matter)... but an engineer with base of 11/11/12 is much better than an engineer with 9/9/12?