Yesterday I spent about 2 hours tweaking my Matryoshka, with the sole intent of testing its functionality as a plain octave and bit crusher effect.
Contrary to what I've read somewhere in this thread, the Matryoshka CAN be used as a plain octave pedal, and I must say it does a pretty convincing OC-2-esque kind of tone. In terms of tracking and sound, it's not as good as the real thing or my COG T-16 (imho), but definitely usable. And it does A LOT of other stuff, so I can't complain.
I don't have the pedal here and I hope I remember all the settings. Please ask if you have doubts.
Octave
Like shown in the guide, simply use the arpeggiator mode, crank both "oct" and "out1" knobs to 100%, everything else on 0.
If you want more presence/sharpness in the attack and/or a more "quacky" sound, play with the "res" and "sens" knobs until you find a tone you like. Everything on 0 is a good starting point, imho.
Even if "clean" and "out2" are set to 0, you should get around unity gain with these settings, because the arpeggiator mode has the hottest "out1" output.
If you want more overall volume, just blend a little bit of "clean" and/or "out2" signal. If you blend some of the "out2" signal, make sure to tweak the "ctrl" knob to get a usable sound. It's an arpeggiator, so good luck with that.

Another good solution would be to not involve "clean" and "out2" at all and use a clean boost, an EQ, preamp or any dirt pedal after the Matryoshka to boost the overall volume. OD and distortion are my favourite, fuzz is good too (especially if gated!).
This is a starting point for a good, simple bass synth tone imho. Add a little bit of clean signal if you want and experiment with the settings.
I must test the pedal at rehearsals, but I'm confident it will work for this application.
The bitcrusher settings I've found are the following.
#1 (BugBrand-esque tone, normal octave)
Mode: b.c.
Sens: to taste (it depends also on your intstrument's output and your dynamics). I like it around 10 o'clock.
Oct: 0.
Res: around 1 o'clock.
Ctrl: around 10 o'clock.
Clean: To taste. I like around 11 up to 1 o'clock for more clarity.
Out1: 100%.
Out2: 100%.
#2 (OC-2+Bit Crusher classic combo, -1 octave)
Mode: b.c.
Sens: see above.
Oct: 100%.
Res: see above.
Ctrl: see above.
Clean: 0%.
Out1: see above.
Out2: see above.
If you want presence and clarity in the attack, keep "Res" around 8/9 o'clock in order to get a high-pitched crushed tone that cuts through the mix pretty well.
Hope this helps you guys.
Cheers.