There would still be concerns at such high levels even if the filtration is on because the aircraft filtration system would not be able to deal with VOC and related gaseous stuff.

Correct, although the health consequences of short duratiok exposure to those compounds would be relatively small, vs for example taking away a new infection.

My personal experience is that in cases which such high CO2 levels (during boarding) the ventilation and filtration is just off. So not wearing a mask is just insane.