I think it looks off because the sinks are not yet installed. Once they are it will make sense and look right.

In the perfect world I would have them flip the vanities so that both have the drawers on the outside edge and the sinks on the inside edge. That would allow the lighting to be more flattering, beside the face rather than above the face. You still might be able to, having sconces at four points across the wall, at each of the vertical bands between the mirrors. Unfortunately the electrician has probably wired already for the overhead lights. My backup suggestion is for a third overhead light over the middle station, which I think would remedy this unbalanced look. If we could back up six months, I would say think of this before the build starts, but that is very easy for me to say now.

This is an option too if you can find matching sconces.

Yes, the electrical outlets are in the drawer

How many people will be in your master bathroom to experience your perceived weirdness pertaining to the light locations? What you have now will most likely function well regardless of how you think it looks.

This is argument for hiring a competent interior designer.

Sorry but how did this happen at all. Where was the lighting plan and why that lower counter at all I do Ikea Godmorgan vanities all the time big drawers not issue with the lightin above the cabinet and aslo the sinks are usually centerd on each cabinet where i use mulitple ones . I guess you takk to the builder but I cannot see that being changed witout a big cost to you. Maybe just much longer light bars to use the same elctrical but light the whole space above ecah high cabinet since I assume that is a makeup area where you dropped the height what are you planning for lighting there I see no plugs there at all where you really need good lighting.

Just add 2 or 3 sets of lights across the top

You'll probably get used to it, but ideally I would want the lights centered over the counter as opposed to over the sink. Possibly going with a wider 4 light versus the 3. But it's probably not trivial to move the electrical that far at this point and I would think hard about living with it as is.

Also the best option is probably to add a light over the makeup vanity as Paul suggested.