The events of TFU occurred before a New Hope, 3 BBY - 1 BBY and the events of TFU 2 occur in 1 BBY. So before a New Hope all those Jedi Starkiller hunt down are dead and Rahm Kota for a time is presumed dead and never actually meets Yoda or Obi Wan. Whatsmore, there is still a year between the events of a New Hope and the end of TFU 2 and I assume in that period Rahm Kota dies and Vader escapes. As for that stuff about Starkiller visiting Yoda, for one he was a clone and secondly he could also easily, and probably most likely, have died between 1BBY and 0 BBY. I expect this will all be cleared up in TFU 3 or some other material and the Star Wars timeline will continued unpeturbed.
doesn't matter if he is a clone or not the fact that he is more powerful with the force then Vader or Skywalker should have been a huge tip off.
Yoda wants to destroy the sith and this guy just strolls on through with the ability to pull a Star Destroyer out of space? Even Yoda can't do that.
Of course then we have the opening crawl of A New Hope which invalidates anything that could be considered a victory for the rebelion.
of course we shouldn't even be having this discusion if it was done right. A good continuity shouldn't leave room for interperation.
Which is why I'm happy that they are relaunching the EU at least the Post ROTJ EU