If the junction box would be accessible from the attic, you can simply turn it around and patch the drywall hole in your ceiling.

Plenty of people have done pretty chandeliers over vanities and that would probably work better than an island fixture unless the vanity is especially long. An island fixture could work over a double vanity if it were long enough or possibly over a tub if it were high enough.

Actually, I was wondering something similar - the builder didn't center the wall lights over the sink locations, since I have to move them anyway (and vanity butts into the corner, no room for sconce on the right hand side), I was wondering if I should pull out the receptacles on the wall, patch the drywall, and put in 3 boxes on the ceiling for pendants that I already have? We have attic access.

How far to sides of mirrors (1 over each sink) and how low to hang the pendants? We have 8ft ceilings, not sure where top of mirrors will be yet but I assume you don't want the light(s) in front of the mirror, but can't go "eye level" like you would with sconces even if they're to the side(s)?

We have a similar issue with the vanity being in the corner, so sconces are out. I have seen several island lights as long or short has light bars you hang above the mirror.
If I could get DH into the attic he would be putting in a sky light. My biggest concern is if the junction box will get the fixture far enough away from the wall. I don't think a chandelier will throw light the way I need it to.

How far from the wall is the box now? Another alternative is track lighting. I have pendants on a track over my island. The box can be anywhere along the track, doesn't need to be in the middle.