Well, the Original Series
was several years before the General War (about 10-15 from the nebulous "mid-war" point at which the ships are selected from) and pretty much every ship in the game has received Modernization and War-Readiness refits just before and during the opening years of the war. IIRC The D6 had its rear shields beefed up a tiny bit and it's boom Ph-2s upgraded with better Gyros to Phaser-1s.
This is obviously why the D6 looks slightly different, yeah!