Depends. If the lights are for specific tasks, such as illuminating a work area, it should be as close to directly above the work surface as possible. An eating area does not need such direct light, so I would tend to make sure you have sufficient light on the areas where you will be working -- food prep, cooking, etc. -- and not worry too much about the eating area. If they are dim-able (which I highly recommend) I bet you find you will turn the lights up for cooking, and down for eating.

On the other hand, if you don't plan to use the counter top as a work area, I'd probably center the lights on the overall structure, as I think that would look better.

Don't worry about what's "generally accepted." If you like how it looks and works, it's good.