Allow me to offer my opinion on this as someone who has been flying electric RC for a long time:
As long as the motors are operating properly at speed, your Phantom is flying smoothly and responding properly to your commands, and barring any odd noises or elevated temperature from a specific motor, I do not believe this is anything you need worry about. For those who have never built an electric RC, each electric motor is controlled by an ESC unit - an electronic speed controller. The ESC feeds power to the motor, and delivers the throttle position information from the controller. When you build a new aircraft, you calibrate the ESC to the controller, so that the ESC recognizes where the 0% and 100% spots are on the throttle. Every controller is different, so this allows the ESC to learn the positions. There is a procedure specific to each brand ESC for how to enter the calibration mode and complete the procedure.
In a single-engine aircraft, you have but one ESC to calibrate. The Phantom, however, is a multi-engine aircraft, with four engines and four discrete ESC units. Were I building a multi-engine, manually-controlled, aircraft...say a four-engined B-17 bomber...I would, one-by-one, plug in each ESC/engine combo, enter the programming mode, and calibrate the throttle for each in turn. That way, when I go to 0% throttle, all engines stop. When I go to 100% throttle, all engines are running wide open. This way they are all running at the same speed, so as not to induce any imbalance into the system affecting the aircraft. In some very high-end multi-engine RC aircraft, they have have individual throttles, like in a real plane, so the pilot can balance them manually. In general though, most multi-engine RC aircraft have but a single throttle, so you want the motors all operating at the same speed. Sometimes you can program all of the ESCs at once, but I believe most seasoned pilots would choose to calibrate each motor individually.
The Phantom, being a multi-engined aircraft, needs its ESCs to be calibrated also. How to enter the calibration mode for a Phantom's ESC I do not know? It may pass on ESC calibration information when you perform the process in the RC Assistant and Assistant software? I doubt this as a usually ESC emits tones indicating it is in a programming mode, and confirming success. But, unlike a fixed-wing aircraft like a B-17, you don't control the Phantom's throttle in the same way. When you issue a full climb command, the NAZA is actually controlling the throttles of each individual engine to keep it oriented to your throttle/stick commands. Thus, even if at idle one ESC is slightly out of calibration, in flight the NAZA will still adjust the speed of each specific motor to make the aircraft conform to your control inputs. As the voltage/current of the battery drops, minute variances will become more apparent in an idle situation. But in flight, the NAZA flight controller will compensate and increase motor speeds as necessary.
You might want to try re-running the calibration procedure in the RC & Software Assistants. That may help, as many of us probably calibrated before our first flight, and haven't calibrated since. The engines break in after a few flights, and the Phantom 2 engines run a lot more than a typical RC airplane with her long flight times. Unless you notice your Phantom is not responding to commands properly, or flying erratically, I do not believe one engine being slightly faster or slower at idle is anything to worry about.