Yes, but that quench area is a lot smaller then on those older engines. The D-shape is cast into the chamber to aid low speed cylinder filling from the primary intake runner, as you said, but it can be removed from the chamber if the secondaries are gutted to aid better high end RPM breathing for racing applications... Especially to unshroud larger 3L valves in the 2.5 heads.
You're right about the gasket though. The only reason I would be worried about putting a copper head gasket on is if I were worried about blowing out a stock head gasket, which are metal already and can take quite a bit more boost than old fashioned paper or cork steel ring type gaskets before blowing out. Copper gasket on Duratec = wasted funds.
