Assuming That the Factors actualy have FTL cabability idependant of the Pandora Gates how then dose it work?
Given Eclipse Phase's genre of Hard Space Opera that limits the available methods of FTL.
Now using Theoretical and Fringe Physics as a base what methods of FTL might be possible.
Negative Mass Drive : Factor particle physics/quantum mechanics is advanced enough that they can control the Higgs Field. Giving them control over an object's effective mass. They can bend Mass of Object until it enters a negative state mass state;the objects effective mass is now less than nothing. This circumvents the blooming of an objects mass to to infinity predicted by Einsteins famous equation E=Mc2. It all also deals with time dilation brought by nearing the speed of light because with in the region of massless space that the ship occupies Light Will Go Faster. Thus the craft never exceeds the speed of light because the speed of light raises with in the Mass Effecting field that it generates.
Hyperdrive: Heim theory is correct. And The Factors can exploit it's principles to create artificial gravity by converting electromagnetism into to gravitational force. This field of electrogravitic force is used to propel Factor ships with out the need for reaction mass. And when the propulsion field is precisely controlled the ship is shunted into a Higher Dimension(Hyperspcace) enabling interstellar travel in reasonable time frame by circumventing normal space geometry.
Warp Drive: Their is a way to fold space without having burn a literally astronomic amount of energy in the process. The Factor have this sufficiently Advance technology. No object can accelerate to a speed exceeding the speed of light, the fabric of space however can expand or contract at rate exceeding the of light speed. A Warp drive would warp space around the ship. Expanding space behind it and Compressing space before it. The ship would remain stationary and by propelled through cosmos by the distortions.
Agatha's law: Any sufficiently analyzed magic is indistinguishable from science.