It should be in theory possible to have pulse width and shape separated in the mod matrix. They’re handled separately in the hardware, it’s just the single knob user access to those parameters that’s mirrored in the mod matrix right now.
It could even be possible to make Sine Level, Saw Level, Pulse Level and Pulse Width all independent parameters to allow for wave combos not possible with the shape knob, like sine + pulse, or saw + PWM. That assumes the waveform VCAs are controlled with separate DAC CV channels, which I would think they are. This would open up the synth into not just Juno, but SH-101 sound design territory.
The TEO-5 gives you independent waveform selection, but not independent waveform levels. It also gives independent PWM.