Theory: saints row and red faction do take place in the same universe, but the red faction games are in the timeline where the boss goes after killbane in sr3.
I know the devs have alleged that the references are just easter eggs and all, I don't care. The timeline adds up if you look at how things play out in the alt timeline. We know that in the timeline where the boss goes after killbane, earth does not get destroyed during the zin invasion, because of the enter the dominatrix DLC, because the saints defeated the Zin absurdly easily, and somehow Shaundi returned.
Beyond that we don't have any clear info on what happened next, but we do know that during SR2 ultor was already working on going to the moon, so it's reasonable to assume that about 20 years later, they were already there, maybe setting up, maybe already doing mining (I don't know how fast their tech allows them to make progress there).
Meanwhile, after the Zin invasion and the events of the dominatrix, the saints now have some space traveling technology, and a reason to prepare for more alien invasions, so they take it upon themselves to protect the world from extraterrestrial threats, and eventually rebrand themselves to earth defense force.