From my perspective, "Form follows Function" (sometimes the other way around for others). I looked at your kitchen layout and photographs and these are my questions and comments:

1) Where did this rule that the sink has to line up with the cooktop come from?

2) What is the door swing opening of the refrigerator? The plan does not coincide with the photo, it looks like the fridge is within a cabinet and set more backwords than what the plan shows. Is the 3'-91/2" on plan still current?

I don't care about the non alignment. You will not be constantly positioned in the dining, on the center line of sink, to see that it does not align with the cook top, sometimes you move around. More important is the clearance in front of the fridge.

That is how I would have planned and designed it.

Is the island already fixed in place? I do not know how much or if you can push the island even further up before it impacts the other point of access on top, I would prefer 2'-8"-2'-10" (a rather large person passing at the same time the refrigerator door is open). 2'-8" width of a door is a minimum per ADA code, not that it needs to be considered here.

I'm sorry, I thought this was about the stove top and the sink not aligning. Moving the island toward the refridge is really not a good option... I'm not a builder yet I'm getting lost on this.

Not having adequate space between the fridge (and pantry!) and island would drive me crazy; a sink that doesn't line up with my cook top would not. One is a functional problem that you will be aware of on a daily basis, the other is purely aesthetics. I don't think it is even something people would ever notice, and once it is all complete and you start living with it -- you may not, either. I would leave the island where it is, and move the light fixtures.

Uh... why should the sink be aligned with the cooktop ??? Is that something people actually notice or think important?

Asymmetry is your friend. Embrace her.

Your island is too long. Adequate clearance by the fridge results in a non starter pinch point on the other end. The overhang on the short side has to be eliminated. Also. Where is the required electrical on the island? Normally, islands aren't moved around willy hilly because the attached wiring wont let that happen. Not to mention that the drain location isn't really movable either without effort and expense, and that dictates sink positioning.

Alignment of sink and range is completely over rated. If it's even rated at all.

You would have the lighting placed over the island.... aligned in proportion over it regardless of where the sink is.

@Sophie Wheeler -- I think you're imagining a "pinch point" -- there's actually a hallway on that end in the photo (not really in the diagram), so they're not in any danger down there.

Am also amazed that the island can be pushed around after drains and electrical have already been run. My contractor would be in conniptions about changes at this point. Design as long as you have to, then build in a hurry before you get any more ideas. ;)

I think pendants should be arranged over the island and it shouldn't involve the other cabinets.