They will all work together successfully, but its going to take some work on your part to hook them all together. The controller board has more than just the Arduino Mega and the ESCs on it- it also has power switching, +5 and +3.3V power supplies, drivers for external loads (the lights), and a level shifter to convert the Mega 5V I2C bus to the 3.3V I2C bus required by the compass/depth sensor. None of these are rocket science- you can download the schematic off of our GitHub site and figure out what you require on your own. If this all sounds like a fun project to you, then just buy the individual pieces and enjoy the project. If you would prefer to have something running without all the fuss, then I’d recommend getting a controller board, even if you don’t need the ESCs.
Note that you don’t need the topside interface if you’re communicating to your project over Cat5 cable or the like. You only need the topside if you use the HomePlug protocol to talk over your tether. If you do this, you need to add a set of Homeplug adapters to your shopping list.