There are one or two scenes that are slightly different. But overall the main difference is that the DVD has DVD quality video. There is one full color video on the DVD that can be watched that doesnt show up in the game. In game its a low res VDU video. But that is also available in the CIC's files section.
The WC4 DVD version does not contain the Speradon shipyard video sequence as seen on the CD version, although in its place the DVD version includes a brief sequence of the Intreprid jumping in-system and then joining up with other Border World's capital ships -- IIRC, two destroyers and one cruiser. This new video is similar in purpose, but quite different in style to the latter part of the Circe tank video sequence, in which the Intrepid is seen jumping in-system to link up with two destroyers and a cruiser after three Vindicators return from a bombing run.