@Kiwisaurus : again, try to read carefully before asking...
Full firmware contains specific drivers etc for the Mark 4, while KoboRoot.tgz contains more general stuff.
Most of the hardware related stuff is in the upgrades directory. Using the KoboRoot.tgz is pretty safe though there is a risk which I rated as fairly low
What I make from this is : A full firmware update contains a directory with device specific files (different between the available Mark's), and koboroot.tgz containing the common bits for every Mark.
So what they did (I did it also actually), was taking the latest hardware update for their device, combining it with the latest general software release, hoping that no special hardware bit is needed by the latest software update.
Hope this makes sense.....