IMO, they need to distinguish between places where icons are peripheral "chrome" and places where the icons actually represent what in the context of how you are using them is effectively "content" that you care about.
e.g. it makes sense for the standard toolbar buttons at the top to be de-emphasized (and for there to be fewer of them, bravo!) as the vast majority of the time they're on screen, I care about my code and not about the toolbar buttons. It doesn't make sense for the GUI controls available in Toolbox, for example, to "fade into the background" - presumably if I have the Toolbox open, the available controls are something I care about. Or if they're not, why is the Toolbox there taking a third of the screen? If you ever have a situation where two-thirds of the screen are consumed by "de-emphasized monochromatic chrome", you're probably doing it wrong - if they're not important you need to figure out how to reduce their physical screen presence, if they're important you can / should give them a more distinctive presentation.
e.g. it makes sense for the standard toolbar buttons at the top to be de-emphasized (and for there to be fewer of them, bravo!) as the vast majority of the time they're on screen, I care about my code and not about the toolbar buttons. It doesn't make sense for the GUI controls available in Toolbox, for example, to "fade into the background" - presumably if I have the Toolbox open, the available controls are something I care about. Or if they're not, why is the Toolbox there taking a third of the screen? If you ever have a situation where two-thirds of the screen are consumed by "de-emphasized monochromatic chrome", you're probably doing it wrong - if they're not important you need to figure out how to reduce their physical screen presence, if they're important you can / should give them a more distinctive presentation.