Don't mind the current order of things. The buttons are generated through a loop that gets the button names from a template file which isn't ordered to suit this action bar in its current state. Consider this an artifact of the mockup and not something that was planned. The same function call that gets the controller layout is also used for a lot of other things, which is why they are not intuitively positioned.
Making the modified buttons smaller might work, but visible cooldowns (charge / normal) have to be kept in mind, along with a clear enough icon to show which spell it is. It also needs room for macro text and the charge counter. Another way would be to reduce the main buttons, but I feel like they should retain a larger size because they represent the current action of the button.
Looking at this image without the modified buttons, it becomes very clear how much room one of these clusters take up on screen currently: