The short answer to your question is "yes".
The UberCats are retired. They can no longer be purchased from the main store. They were a limited edition, featuring a limited edition eye. But as you point out the Tigres still carry their LE traits... they are not listed in the same "retired" category because you can still go to the Main Store and buy a Tigre. You can also still acquire a Fancie cat through the jewel-collecting process. They are not retired.
But most LEs are retired, like the Scarecrows I mentioned.
The trait database doesn't forget what old retired or Limited edition traits are. Certainly I don't know how the programming works, but it doesn't seem so difficult for there to be something like:
If Scarecrow Then traits a, b, c.. available. If UberCat then traits: hidden eye =Uber Odyssey.
If you mate two Korns today you will still get a Special Baby that is guaranteed to be a particular costume Megapuss.
I don't think it's that hard for KittyCats to make these kinds of specifications.
I do think you're right that the UberCats may be a somewhat special case but I don't think that they're so different from the fancie cats which are guaranteed to carry their particular eye (if indeed all UberCats hide the Uber Odyssey).
You sound frustrated, as if you want your unrezzed Ubers to be able to carry all the new Fall traits. But I think it's reasonable to gather that they won't carry new eyes. If freshly rezzed the SLB14 cats will carry new traits available to all Starters yes, but not any Limited Edition traits from the Fall Collection, which will be exclusive (as Uber Odyssey is exclusive to it's own collection).
Yes, the word-wrap issue is annoying.