Yeah, that surprised me too (though I'm a mechanical engineer by training and not a EE - so don't quote me when it comes to electronics...
). The article suggested that it may not work for all transistors, but in this case, as long as the signal somehow finds its way from the base to the emitter, I guess it can be amplified by the subsequent op amp stage.
However, after studying the online schematic (assuming the schematic is correct), the Mudhoney is really nothing more than a modded Proco Rat. The BJT buffer can probably be removed entirely and it probably wouldn't affect the sound at all. The buffers (including the input buffer which remains on the vero layout) are simply a part of the bypass circuit of the original effect (which is quite elaborate, according to the schematic).