Nope - displacement is how much volume is "displaced" when the piston moves up and down. The combustion chamber volume is the volume when the piston is at top dead center. The RATIO between top dead center and bottom dead center is compression ratio. The VOLUME between top dead center and bottom dead center is the displacement.
Yes, there is less total volume at bottom dead center (12.1cc less due to the dome on the xb9 piston), however the same decrease in volume is present at top dead center. This is why the displacement does not change, but the compression ratio does.
Trust me, I'm just a random guy on the interwebs ;)
In all seriousness, do a search on google and you'll find the difference explained with pictures - probably in either a wiki or a how-stuff-works article.