JTA was not based on Star Wars Rebels. If it has been "re-imagined" to that it's the definition of a convoluted backstory.
The "Trials of the Temple" re-do is indeed based on SWRebels. That's why it included the Seventh Sister, who is a character from SWRebels.
I'm sorry you think it's convoluted. Those who have seen Rebels or pay attention to the show's dialogue should ordinarily not have any confusion as to what's happening.