"Many developers used the colors of the default theme no matter what"
Which is what they were supposed to do, resulting in usable software that honored the user's preferences. And developers didn't have to dick around with color palettes. Win/win.
"Others used the Windows-supplied colors for the background color and maybe the main foreground color, then used fixed, non-customizable colors for everything else, making everything invisible or hard to see if you used anything but a white-ish background"
Yep, some did. And? If developers issue defective software, the OS should be degraded? What's your point here? Let's say developers somehow mess up sound reproduction: Should the OS no longer support audio playback?