Grant, that sounds like TMP, not The Wrath of Khan.
The new effects for the DE of TMP were done at 480i, mostly using LightWave and other software.
For TWOK, the footage exists on film, and thus Nicholas Meyer's extended cust could theoretically be be done.
It is likely that the films on Blu-Ray are the theatrical versions of the film for consistency of the set, and to avert consumer confusion.
I think I read somewhere that TWOK went through some kind of restoration process beyond a simple transfer and cleanup of the other films, but I don't think they did much to the the films.
No, I am referring to TWOK.
When questioned by Bill Hunt as to why they didn't release the extended versions of TWOk and TUC on Blu-ray in 2009--they told him that they didn't realize until too late that they didn't have the extended footage readily on hand to be transferred to HD 1080p. So they simply released the original versions only.
TMP is a totally different story where they have yet to render the DE new FX in 1080p.
That would require some work, whereas the 3 and a half minutes of NON fx footage added to TWOK and TUC would be simple to transfer to 1080p and edit into the movie.