I think it might be possible to resolve this issue without removing the feature: if only a foreground color is being used, mIRC will check for duplicate foreground/background colors and fix the foreground color if necessary. However if both a foreground and background color are used, no check is performed.
Does that make sense/sound reasonable?
As someone who used the default mIRC theme with color tweaks for over 10 years, I have to agree with this option. I always wanted the feature but it was just too much trouble to write a new theme just to have it.