I find the "do not assist queue" option great. I then only change engineers accelerating docks when my resources start dropping to fast, or my reserves just keep increasing. Its very low maintenance, but I can still safely keep a good number of engineers around for repairing large fleets.
Right, I'm in the same camp, and usually I research Mk.II Engineers purely for FRD duty; leaving all of the Mk.I's for static build boosting assignments. The greater range on the Mk.II helps keep them out of harm's way, and their faster repair rates means they can shove off quicker.
I set his rebuilders to an FRD point as far away from the turrets as possible. If the AI ships are killed fast enough, then the engies/rebuilders don't arrive on scene until the threat has been greatly diminished. This meant that there was a bit of a delay in their response, but they also had less AI ships targeting them once they got close to the turrets. Hope this tip helps.
Interesting idea, though having them so far away they can't get there in time for emergency repairs would make me a bit nervous. I manipulate FRD "home" points all of the time to optimise their movements, but never thought of putting them in the Oort clouds.
I think what techsy730 points out is the "change" I'm seeing, though. It's not that the engineers are really doing anything different, it's that the AI now takes pot shots at them whenever possible, even if they are under fire from military units.