RG: This is correct; C6 and C9 also have a varying impedance, and serve to lower the gain and hence the amount of clipping at lower frequencies. Making this smaller/bigger, causes less clipping at bass/more bass to be clipped.
While I'd hope this is well known around here I'd also like to add that the difference between a 47nF cap and a 1uF cap in C6 and C9 is huge. At the smaller end you can have a very boomy big muff that doesn't do chords well on the low E/A strings, at the other if you have 1uF's in there it handles chords very well.
A lot of people find Sovteks boomy as hell, that's primarily because of C6 and C9 being 47nF (some triangles/ ramsheads are affected by this too with C6 and C9 being 50nF) and once you up them to 1uF the boom is gone. Another thing to note is that once you up C6 and C9 it will give the impression of having less bass overall so you may need to increase the majority of the .1uF caps to 1uF also to compensate.
A good place to have the .1uF caps is C4 and C11, use 1uF for all others.
In some cases, and it is always individual pedal dependent and also what amp you're using to a certain degree, you can get rid of the boom sufficiently with as low as 220nF caps in C6 and C9.
C2,5 & 8 determine the high frequencies cut off point. The higher the pF the less highs come thru. Try replacing the 470/560pF caps with 100pF (or even 50nF) for more high freqs while at the same time retaining the scooped mids of the trademark tone stack and the same bass level. Doing this is particularly useful in an un-ordinarily dark sounding big muff.
I really have no idea why things do what they do in any circuits, I just know what does what from personal experience learned from trial and error.
This thread is great BTW, I can finally learn the technical reasons behind why things happen rather than just knowing that they do happen!