... Well, the colors aren't the exact same as in the raster version, if that's what you mean (though I wouldn't say they are quite as different as your picture shows.. only a little dimmer than the original, which is a typical side effect of quantization).
However, the colors in a trace with the Stack option on are completely identical to the ones in a trace with the Stack option off -- ie. the Stack Scans option does not affect colors at all. I can post a comparison if you want.
Checking up on this reminded me that the Preview pane in the Trace dialog should show exactly what colors you are gonna get, since it displays a thumbnail of the 'preprocessed' image (in this case, the image after it has been quantized to N colors). It's interesting to note that in all frames of your tutorial the thumbnail shown has the reddish tone.
FWIW I'm running inkscape bzr r15625 (ie. trunk, which will eventually become release 0.93)
EDIT: I think I was tracing a different image than you meant though, I'll retry.