Well... In my opinion the bottom line is that they want to gently encourage you not to change the clip background color.
You've got frozen tracks; muted clips; clips not in solo'd tracks; regionFX clips; selected areas of clips... there's just so many subtle color hints that ideally need to work together to convey meaning to the user - especially new users.
It's so easy to screw that up by color customization. Also, you've got the "track follows bus color" feature that is pretty nice.
Also, there's the whole "let's differentiate our look from the other major DAW offerings" which mostly seem to use color background and black waveform'd clips.
I'm in the group of folks who prefer "black wave on color clip" but I appreciate the reasons why the change was made for X3.
In my experience so far, it's been more rewarding to not fight it, but just go with the flow, and get used to the dark clip and light waveform appearance. I actually prefer it for MIDI clips. I like the colored notes on dark background, especially when I have multiple tracks selected in the PRV and the colors match the track view.