I have two sets of lights over my island. neither of which is truly centred, but positioned very purposefully.
On the working side of the island I have a couple of pots which are placed so there is one directly above the sink, and the rest equally spaced from there. They are positioned roughly centred depth-wise on the centre of the working side's cabinet depth, but not the entire island.
On the seating side of my island I have two fixtures, each has three smaller "pendants". The two fixtures were positioned so that the spacing between each of the 6 lights is identical, and that leaves some space on each end that then is not covered by pendants. Depth-wise they are positioned essentially along the imaginary longitudinal line at the rear of the eating space - I have a 12" overhang, so they are essentially placed 12" in from the edge of the island.
That's the long answer to your question. The short answer is no, mine are not centred, but they are positioned on purpose with function and symmetry in mind. It sounds as though yours are not. In my case the KD was VERY specific about where each light should go. It was written clearly in her plan and we did a walk through with the electrician when all the studs were visible so he had no questions.
Sounds like a failing on the part of your KD in my opinion. So frustrating when you are counting on the professionals you employ!
With some of the details that haven't gone exactly as I imagined in my remodel I realize that most of them are liveable. For example, if it were pot lights that are recessed into the ceiling it might not matter. But pendants are hanging in full view...I think if it's really bothering you you need to see what can be done with the least amount of damage to your new ceilings in order to fix them. Make sure to meet with your KD and show her how "basically" centred (i.e. not at all centred) her plans really are, and see what kind of magic your contractor/electrician can muster up for you. Or if there is no magic, with any luck you can have the KD pay for having it repaired and done to your satisfaction.
Good luck!
Q