Update
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I made a simpler patch to demonstrate the issue: Osc3 set to sine, octave +/- 0 and mix level 32, everything else off (no filter no nothing.) In the modulation matrix, modulate Osc3 mix level with Osc3, modulation intensity at 32.
With keyboard at "normal" without transpose, the two lower octaves (C3 - C5) sounds as expected, the issue sneaking in in the last octave above C5 at 524 - 1048 Hz. Try transposing up two octaves up to 4096 Hz and it goes completely bonkers. The bad news here is that all the internal DACs runs at approx 1100 Hz, which is terrible. In fact, I'm suspecting this is an OS programming error rather than a conscious design decision.
The good news is that the ADCs and the passthrough to the DACs and CV jacks on the backside, against all odds, are full range. You can do your audio rate filter modulation proper using an external filter and bring it back through audio in. Wave folding is a little more involved since every little digital artifact from the DAC gets magnified to the extreme by the folder - yes, the analogue oscillators are sampled before being passed on out. Manageable when you have a filter in front of the folder though.