"Controls" could be any number of things. Shows like this, especially those with show elements spread out over a large distance, have multiple smaller show control systems that are linked into the show lighting, audience area lighting, fountains, hydraulic lifts, pyro, and whatever else in the immediate area. These sub-controls are then connected to a master controller which often does nothing but send out a single timecode and "go" commands so that each sub-controller runs its' pre-programmed cues in sync with all of the over sub-controllers.
To paint a parallel picture, you have Reflections of Earth. Every barge on the water has its own controller. The show lighting in each country in connected to a controller local to that country. The searchlights on top of the various countries and Innoventions buildings have their own controllers. The main show control in the Mexico booth runs the master timecode, but each pavilion controller knows when in the show to turn on the strobes, to turn on the edge lighting, etc. All it needs is the "start" command and to keep its own clock synced up to the master show controller. Each sub-system can also be manually inhibited by techs if something malfunctions.
To get back to Rivers of Light, since there is a live talent element to the show, master control will most likely be in the middle of whichever direction the show plays to so that the stage manager can keep an eye on the overall show, just like the Fantasmic tech booth is in the back center. This means the RoL tech booth with most likely be in the Nemo to EE stretch.
And since the Tree of Life is WAAAYYY on the other side of the lake, it needs its own sub-controller to handle any effects installed on the Tree, even if it's just a few twinkle lights and the ability to dim the Tree's floodlights up and down.
(Sorry, didn't mean to make this post quite so darn long...)
-Rob