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.