How did Conduits end up imprisoned after Infamous 2?

Question

Infamous: Second Son takes place seven years after the events of Infamous 2, and during those years the United States formed a Department of Unified Protection (DUP) in order to imprison Conduits (who are branded "Bio-terrorists").

However, I don't see how this could have come about with either of the two endings for Infamous 2 (good or evil).

If Cole chose the good ending in Infamous 2 then that means he

activated the Ray Field Inhibitor (RFI), which ended the Ray Field plague but also killed himself as well as many (all?) other Conduits. The ending specifically mentions that Conduits overseas were killed by the RFI (which is shown emitting a blast that can be easily seen from space), even if they didn't realize they were Conduits (presumably because they had the Conduit gene but it hadn't been activated by a Ray Sphere).

This suggests that

all people with the Conduit gene were killed, which means there would be no Conduits left to imprison after Infamous 2.

On the other hand, if Cole chose the evil ending in Infamous 2 then that means he

destroyed the RFI and became The Beast. It seems impossible for non-Conduits to win a war against Cole plus all the other Conduits and imprison most of them by the events of Infamous: Second Son only seven years later (especially with no RFI to stop the Conduits). Moreover, non-Conduits would also die off due to the Ray Field plague yet the plague does not seem to be a problem in Infamous: Second Son.

Either way, it doesn't seem possible for non-Conduits to start imprisoning Conduits in the years between Infamous 2 and Infamous: Second Son. Which Infamous 2 ending is canon (good or evil), and how did that ending result in the state of affairs in Infamous: Second Son?

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Source for the hidden image above, and video of the Infamous 2 good ending (starting at 2:58:27):

Answer 1

Which Infamous 2 ending is canon (good or evil)

The story revolving around Paper Trail revealed the RFI had a 90% success rate, leaving 10% of survivors. This implies it was the good ending that is canon for inFamous Second Son. The website for Paper Trail was deactivated on December 16, 2018, but the in-game story missions are still available

An explanation for why Conduits are still a thing. The Hero ending of the previous game made it seem like Cole sacrificed himself and the Conduits of the world in order to save the majority of the human population. However, playing through Paper Trail reveals that only 90% of conduits were killed.

_Source

The 90% death rate was revealed on the "Test Your Power" trivia quiz that was released prior to Second Son. While the trivia quiz is no longer available, there are videos on Youtube that walk through them:

Approximately 90% of conduits all over the world died when The Beast was destroyed in New Marais. The deaths were so widespread that conduits were believed to have experienced an extinction event. But in the following months it became evident that some conduits managed to survive—even some who were present at New Marais at the time of The Beast’s destruction. To this day, we do not know why some perished and others survived, but we suspect some kind of Ray Field Radiation event occurred.

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How did that ending result in the state of affairs in Infamous: Second Son

Unfortunately, there is currently no in-game explanation to why these 10% survived whereas the other 90% perished. A fan-theory is that their conduit gene was dormant and not present when the RFI went off.

Based on a population statistic on Reddit, roughly 43.75 million people killed as a result of the RFI. Due the chaos that arose, and unsure what conduits were capable of, the DUP likely imprisoned them out of sheer fear