And there's the crux. If there is still Gamebryo in the background, it still is Gamebryo.
My computer used to be a DELL, but then I changed out the Video card, then the power supply, then the RAM, then added a new harddrive, then came the motherbord, which led to needing a new case. Does this mean that I still have a DELL computer? Not by a longshot. I started changing components out one by one till I had a new computer, I still have a couple components left over from my old DELL, but it is in no way a DELL now. The new engine for Skyrim is likely no different than that.
Point is: You can start with Gamebryo and start making changes to things that you don't like or need to be changed, that the final product, while originally based of of it is no longer Gamebryo.
Of course there are those people that will still say that it is Gambryo regardless of how many changes were made to it.