They may have ignored them so that they could use uninterrupted picture/sound from The Menagerie without cutting back and forth between the Menagerie picture/sound and the B&W Cage picture/sound in the space of a few seconds.

For the color restoration, my suspicions are that there is no color negative for those parts. (Or maybe they WERE lazy - for example, even in the modern restorations, they don't seem to want to do the effort to put Malachi Throne's Keeper dialogue back in and still use the higher-quality Menagerie audio surrounding it. I know it can be done.)