FP : The highlight effect on the command buttons is being discussed here. Disabling this effect has of course no effect on the preselection highlighting of objects.

Michael : Wow, the whole UI being driven by CSS is fantastic !! It looks very flexible, I see that there are even controls for button size, and it looks like mouseover even supports fade transitions (hard to tell what kind of fading transition/profile curve it is using though).

Simply knocking back the intensity of the hover states really helps already :
http://i.imgur.com/Lx3Uc09.png

(When the user put the cursor over a UI element, any highlighting effect applied to this element can be very faint because the eye is already looking right there and will be sensitive to even the faintest value change. I believe that the trend consisting of making big UI button flash with a lot of contrast is misguided UI/UX design practice : it looks good when presenting the program to a board meeting or during a tutorial, but for the end user it is not necessary. It does work great when controlling a UI with keyboard arrow keys or a gamepad though, like in Steam Big Picture, the Xbox dashboard, and so on).