The "custom colors" in question are ones defined by "0 !COLOUR" (generally in ldconfig.ldr). LDView doesn't do a good job with these, treating them all as global, no matter where they appear.
You still need to deal with "blended colors" (colors with numbers between 256 and 511). LDView does that in LDLPalette::initDitherColors(). This is done using hard-coded values for the first 16 colors, so redefining color 12 won't affect the blended colors based on color 12.
You still need to deal with "blended colors" (colors with numbers between 256 and 511). LDView does that in LDLPalette::initDitherColors(). This is done using hard-coded values for the first 16 colors, so redefining color 12 won't affect the blended colors based on color 12.