It’s worth reading app note AN008. It contains the following:
Note: When IF AGC is turned on the overall gain will not vary much with RF Gain adjustments as the IF gain will tend to compensate to maintain an optimum level to the ADC.
As the RF gain control is right at the input to the RX, turning the gain down will add noise as the later gain stages add more gain to keep the ADC working at max efficacy. This will cause the observed noise level to rise. I’s also worth noting that the S-meter maintains its reading of incoming signal strength regardless of RF gain setting.