Personally, I think mixing white and bone fixtures makes the bone color look dingy. You can get Toto toilets in a bone color (your Toto dealer should be able to provide you with color chips so you can compare the colors), or you can switch out the sink - find out how the sink is attached to the top. If it's clips and silicone, you'll be able to remove the sink; if it's epoxy you are outta luck. (And if it's epoxy I wouldn't buy it anyway, because how would you replace the sink if you dropped something in it and cracked the sink? You'd be stuck with a cracked and possibly leaking sink or replacing the whole vanity top!) I also think there is absolutely nothing wrong with a white sink in a black top, I don't think it's "too stark" - I think it looks clean, neat and elegant.

Cheap matte paint doesn't clean well. That's true - in general. The better (usually higher price-points) mattes clean like a dream - it's amazing actually. Aura Matte in particular is pretty awesome. I'm afraid I have to disagree about matte finish showing imperfections. Matte is a great choice for hiding walls that aren't exactly perfect and might not have been prepped to perfection. Matte is the next best choice after flat or dead flat for hiding imperfections. Some people simply can not stand to live with flat or dead flat - they need some visual 'slip' to the final finish. Once you start moving into satin finishes I do think it's tougher to hide the bumps and whatnot.

Lutron makes something like 100 colors of outlets and switch covers. I ALWAYS try to match them to the wall color or accent color if high contrast for visibility's sake is needed. Yes, it costs a bit more than the 29 cent white ones, but it's a detail you see (or don't see!) subconsciously when evaluating a room. Just like having a stark white outlet in the middle of your wood island, sure, you can, but I wouldn't. However, if these are new outlets and you are under the gun to make a decision NOW, then just put in white and replace them later with something from Lutron. I'd also put in the wide rocker switches rather than the small flip ones. But either is easy enough to do at a later time DIY when you aren't under as much time pressure. NEVER pay to have an electrician just change out a switch or switch plate. It's about the easiest DIY imaginable.

I don't think it's necessary to match the cooktop to the granite. We have a black cooktop in a light granite, and I think it looks fine but you can be the judge by looking at the photos below. I prefer black for cooktops as black just makes me think of a range top, and the speckled black tops are easier to clean. Here's ours in our unfinished kitchen: