Affect in the sense of either masking or exposing said differences. For instance, let's say we're both listening to the same song from the mix position in our respective rooms and both of us turn up a parameter that provides an overall Level boost along with a 4 dB boost to 90 Hz. Assuming you had a room mode that produced a null at 90 Hz at your mix position and I didn't, would you be able to hear the impact of that 90 Hz boost? No, in fact from your perspective there would be no audible difference between simply cranking the Level control and boosting the aforementioned Level parameter with said 90 Hz boost. Thus, the null affects your ability to hear said boost, but it's not the denominating factor that determines whether an actual difference exists.
