Yes, but only to a certain extent. The 10pf dulls the clean channel. With the signal being passed on when the lead mode is engaged it will have an effect, although minimum. The .001 mod is specifically for the lead channel as certain people, and its designers think it is too bright as well.
Having both would darken the preamp to a certain degree and the tone stack would be altered in how effective it is on the darker signal. It mainly allows you to open up the treble more, and with this being the first control in the entire signal chain it will change the overall tone and increase input signal of the amp and allow the other controls to become more dominant. It is a small amount though. The fender style tone stack really are like volume controls for their specific frequencies. Notice how there is no signal with all the controls down.