I recently spent several evenings re-working all of my colours across all of my computers and screens; terminals, IDEs, etc. Ultimately, despite using the same tools, and always dark mode, across all of my machines, the setup for each was different.

I think it's safe to set a standard colour-set so that it's immediately usable, but beyond that, a user should be customising to their requirements.

Perception differs among people; many of the colours OP listed as unreadable, were barely an issue, bright yellow being the only one I could unequivocally agree on. Perhaps display type, configuration and colour calibration is an important factor, as well as individual perception, ambient conditions, brightness levels, contrast, and perhaps even more variables have a significant effect.

I've also learned, since adding an OLED Monitor to my desk alongside the IPS ones, that it's possible to have too much contrast; brightly coloured text alongside pixels that are literally off can be just as problematic to read at times, as low-contrast.