While it's true that the author wrote stuff into the episodes we didn't see, the only contradiction was the Techomage's transporter exploding instead of jumping to hyperspace. Everything else really might have been going on behind the scenes of "The Geometry of Shadows", but that's not really the issue here.
The real problem I have with the Techomage's depiction in the Dark Mirror is that it contradicts what we learned in ACTA and Crusade. While the spinn-off series might have been a disjointed mess due to WB's constant interference, the basic story and lore are still from JMS himself and that includes the way Technomacy works (in part in the series itself and in bigger part in the published screenplays of the unfimed episodes) and the way they are governed. The same goes for the Drakh which were turned into Dark Technomages in the Dark Mirror, which again contradicts what we learned in the series, the movies and crusade.
I know that Dark Mirror is a different continuity, but they used to be the same until the point where Sinclair was shot out of Delenns field of vision and she had to choose another Starfury pilot, thus the powers and form of government of the Technomages and their history would still be the same as the one in the actual series.
Also JMS himself gave the technomage trilogy a "canon-rating" of over 90%, so I'd say the books do give a good base-line for how he wanted the technomages to be portrayed. Unfortunately all the links to the interview in question seem to be dead by now, so I don't have any proof, just my memory.
What I did find was JMSNews
. While I don't know for sure, this does seem to be genuine. Particularly these three messages seem relevant to this topic: http://www.jmsnews.com/msg.aspx?id=1-6153&query=technomage http://www.jmsnews.com/msg.aspx?id=1-6416&query=technomage http://www.jmsnews.com/msg.aspx?id=1-5786&query=technomage