filter between amplification stages of a distortion pedal
Your assumptions are incorrect and thus so are your conclusions.

(edit) It seems I was too hasty to answer.

The 2N3904 has far lower hFE (>80) than 2N5089 (>400) by a wide ratio 

The result bypassed CE amplifier is that positive parts of the audio wave have more current and also voltage gain than the negative peaks so that the CE amplifier tends to distort towards saturation. This makes it rich in both even and odd harmonics as Vce goes towards saturation, which seems to be the purpose of this guitar fuzz box. 

When lower hFE transistors are used, the 1st CE amplifier could actually be operating with a much smaller signal and thus more linear and not distorting until the 2nd CE amplifier where it could be more likely to be clipping on both polarities with less attenuation perhaps on the gain pot and producing harsher odd harmonics.

Since the range of notes in the guitar is much wider than simply 3:1 or the 3rd harmonic of a square wave, filtering does not seem like the right approach.  


  Increasing the hFE of the transistors in the 1st stages seems to be the strange yet desired distortion desired for this box.