The Pi requires 5V, so that couldn't possibly be the case, right? the left hand side is merely a breakout, a direct line to the GPIO, to feed external components.
... powering a Pi should be done, certainly preferably, via the micro USB provided for that purpose. You could feed power right into the GPIO, providing 5V obviously, but you would be bypassing any protection circuitry on the Pi, i.e it is not a good idea unless you know what you are doing.
If you don't mind me saying, I would highly recommend you shelf your plans to power the Pi via any means but the micro USB until you are a bit further down the path of getting your project under way - introducing a 12V fan already requires some thoughts, and the questions you are asking are starting to worry me, to be quite honest.
Don't take this as a slap on the wrist, but try to take one challenge at a time. Get your fan working, controlled from the Automation pHAT first, then and only then add the complexity of powering the Pi in a less standard manner.