Like stated in the commit message for this, the rationale was PX4 driver: https://github.com/PX4/Firmware/blob/master/apps/drivers/mpu6000/mpu6000.cpp#L372
I could imagine, that using the z axis gyro as a clock reference is more stable because that axis is generally rotated less often than x and y but maybe @peabody124 or @kubark42 have an idea about this.