The difference is that the Star Trek books were never considered canon. Heir to the Empire, on the other hand, was touted as the official continuation of the story.

We never, ever expected them to adapt any of those books into VII-IX. That would've been stupid anyway, "yay, we already know what's gonna happen." But I really don't think it would've been complicated to at least make ST "compatible" with the EU instead of just placing the EU in its own timeline/dimension/whatever.

ETA:

Tobar, that's very cool to read! Could you provide a link or is that from his facebook page or something?