So while Court of Shadows certainly adds new things to the fae mythos in Shadowrun, as far as I can tell it doesn't really contradict what we knew before -- although it may contradict theories fans may have had.
Don't get me wrong there was a strong connection to faeries in all of the English European setting material for Shadowrun and in particular the Irish mythology for Tír na nÓg. So the myths have a true kernel, but it was either deliberately kept vague to make later additional connections to the Fourth World possible or they just didn't yet know in which direction to go. And of course then it got cut off along with the rest of the crossover.
And mind you I haven't yet looked into Court of Shadows, so I can really only base my impression on what others (you among them) have written about it. With that caveat out of the way, now that the focus is so much more on the fae mythology and the Court as a separate entity that existed in the last magical era rather than the reincarnation of some ancient precursor from either the Fourth World or before, the connection to Earthdawn seems more remote.
I'm tracing some of this stuff to build a timeline of clues for various crossover aspects (
see here, will put it on the English wiki later). My impression so far on the background of Tír na nÓg, in the beginning they were all over the place. The
London Sourcebook mentions a dark, anti-human Unseelie Court and a spirit force, the Daoine Shidhe (possibly connected to Tír Tairngire), both opposing the ruling Seelie Court. But
Wyrm Talk briefly talks about "Lady Brane Deigh of the Daoine Sidhe". Which makes sense because I think the Daoine Shidhe are a remnant of the Tuatha De Danaan? Now, that was all before Earthdawn and obviously the portrayal of Tír na nÓg was changed a lot when it got its own sourcebook. I believe the only time the Daoine Shidhe come up again is the scene with Finvarra from the novel that you mentioned. There they seem to be connected to the court, not really an opposing force. Whereas the Unseelie became a social movement or dissident organisation in both
Tír na nÓg and
Shadows of Europe which I always thought was a nice variation of the standard Seelie/Unseelie relationship.
And really it is not Court of Shadows that made the Unseelie Court the more traditional opposing force with mirrored power, but Aetherology.
In regards to the Tirs, i've actually always viewed Tir Tairngire more as the recreation of Shosara and Tir Na Nog as the recreation of Wyrmwood, as noone in their right mind would want to recreate Bloodwood.
Though Shosara got into trouble for being too open minded whereas Tír Tairngire was run by some really xenophobic fellas.

Anyway I actually think the answer is more complicated and probably has to do with shifting ideas about the crossover behind the scenes.