It doesn't matter that my ships are mauled, it doesn't matter that they have to fly halfways across the map through the range of a fortress and a SoD, those stubborn little things insist that mine remains are public enemy nr. one. Probably for aesthetical reasons. As a result I have to non-stop babysit them when I give my group an attack-move order.
Engineers should only clear mine remains if they're a) very close and b) have absolutely nothing better to do
Engineers actually do give the lowest priority to mines. Most likely they are unable to find repair targets amongst your ships doing battle because the ships in battle are still being actively shot up. Engineers can't repair anything that has been shot within the last 3 seconds, so they aren't much good during the midst of an active battle.
However, you have raised one particularly good point here -- which is that when in attack-move mode, the engineers cover the entire map. That decision was made back before free-roaming defender existed, and so made sense at the time. I'm going to update the engineers so that they only look locally when in attack-move mode (so, really, nothing is changed for them when attack-moving), and they have to be in free-roaming defender mode in order to travel the whole map. Thanks for bringing it up!