But even that wouldn't be a problem. With minimal changes there is no reason we couldn't track the CD while we can't see the button. It's hardly an unsolvable issue, with a plethora of possible solutions from showing the CD in a less "blocking" fashion on the button, showing just an outer ring that counts down so you can see the available ability lit on the button, or even with a "popout" button that shows the skill cooling down (though that's a bit tricky given the freeform UI and plethora of skills comparing other games).

Or, ideally, a logarithmic CD-bar like WoW has as a mod for all CDs, but then that's a very complex solution, albeit a very cool one.