I find it's more of a problem when applications use the color palette instead of 24-bit color. Someone might pick foreground and background colors that contrast perfectly well in their 8 color palette, but that in mine are impossible to distinguish. And changing them for one case might break legibility somewhere else. When the colors come from the 24-bit RGB selection, contrast will always be as the author intended.

I've had that problem with the default LS_COLORS/DIR_COLORS settings in some Linux installs. It's very annoying.

If your palette does not have good contrast between foreground colors 31-37 and background color 40, that's on you. If you cange the default background color to something other than 40 that's also on you - if you want the default background to be white, change the palette so that color 40 is white (instead of changing the backgound color to e.g. 47) and make the foreground colors dark enough so that they contrast well.