The only time I've ever seen the dual sensors (IMU's and Compasses) on my Phantom 4 vaguely match each other is immediately after calibration. After that, they happily go their own ways without any problems.
So, I'd only be worried about them on the I2 when one (or more of the readings) is constantly showing red values, flagging an error message, or demanding to be recalibrated. Even then, one sensor showing amber/red while the other is green/amber isn't critical as the green/amber one will be used instead. There's usually a small dot at the right of the text of the sensor in use.