Other major differences are that its engines have dual modes and thrust vectoring capabilities which the original Hayabusa lacks, and the missile hardpoints have been modified to be able to carry other systems as well such as additional sensors or external components. There are also internal frame changes (or additions in the refit version) to handle the higher stresses resulting from thrust vectoring, though they don't change the craft's resistance to damage.
It looks different and larger mainly because of Khas' creative license, added detail, and the fact that a different program was used than DOGA to make the art. I attempted several times to make it in DOGA, but was never happy with the rendering, especially with the cockpit. I was never able to secure assistance with the model to properly replicate the details reminiscent of the V6D, largely because the V6D's model has long been lost.
I've been entertaining this upgrade in some form since the days of the V6C to be honest, and the Tsubame was specifically intended as a testbed for upgrades as far back as two and a half years. I figure it'd be different if the V6D was being outright replaced, but refits aren't that uncommon, particularly if they add functions that aid the craft in its role and feed back from other projects and are phased in gradually as time and resources permit.