Likewise on Unix-like systems: most things can be covered with GTK and Qt themes, but some GUI programs would use a different GUI toolkit, and occasional developers would assume a dark-on-light theme, setting fixed colors accordingly.
Even TUI color interfaces suffer from that: when programs use colors outside of the 16 (that are rather practical to configure) or tweak (e.g., dim, reverse/invert) those for a particular kind of theme.
An annoying thing is that in most those cases things would have been fine if the developers simply did not touch colors. Even the linked article would have been more legible if it had no CSS, with either the usual defaults or a sensibly configured web browser: now it has a text-to-background contrast ratio slightly below the minimum of 7 recommended by WCAG.