Xeno Federation is an organization led by Shining Ginrai. Shining Convoy son come from a dark future where the Equality Act is passed. Causing a turmoil called Zen Seibertron Civil War. Ruining Ginrai childhood and turn his father into a monster that abuse him and train him into a near-emotionless killing machine. Causing Ginrai to resent his mother and the Xeno for taking away his happy childhood.
The organization main goal is not to subduing or conquer Zen Seibertron Teikoku in any way. But to wage a hopeless war against ZST while employ many cruel and inhumane tactics in order to paint the image of Xenos as a bunch of evil imperialistic, fascist, militaristic *beep* that make ZST look like a good guy in comparison.
Another goal of the organization was to capture and torture Setsuna both physically and mentally. With intention to break her and cause her to hate the Xeno. Preferably as much as Shining Convoy, so the Equality Act will never be pass.
However, all that convoluted goal was well-hidden under a false ideology that Ginrai was a savior and the only person capable of defeating Shining. An ideology that reinforced by brain-washing.
Thank to the action of Ginrai, the timeline where Equality Act is passed was removed from existence.
Due to the timeline being linear, and the power of Vector Prime, there is no paradox.