The more I think about this, the more I like it. Since you hadn't finished the book yet, I'll spoiler code how it related to the discussion of the ending.
Control's final monologue, in this reading, can take on that megalomaniacal, delusional bent as soon as you consider that it could be an unreliable narrator. In this context, the epilogue becomes an "I am invincible!" rant given while the villain is dying, but it doesn't go against anything that was established. Remember, the root of the problem was that Uraei altered its own reality to accomplish its aims. The creation of Section 31 was a post-hoc rationalization for what it already wanted to do; if there hadn't been some ambiguous wording in the Starfleet Charter, it would've found some other excuse, and it would've tweaked its own programming to live with it. In a human, we'd define that kind of thought process as a sickness; altering its own guiding principles, personal history, and norms of behavior by its whims, and with such conviction it would believe it had always been this way. Delusional behavior, or compulsive lying, or sociopathy. And, hey, Control can reasonably take credit for everything that ever happened, so long as someone involved used a computer at some point. They aren't even big lies, more retcons of its own past aims.
In that case, the epilogue is Control's own dying thoughts; "Yes, this is exactly what I wanted to happen from the start." Everything is going according to my plan as my mind is being eaten alive. It's really all for the best. The line about Control's "new configuration" having been in testing for five years is a bit weird, in both this reading and in the apparent interpretation. Though, the Borg Invasion was five years prior; perhaps the "new configuration" is referring to its own nonexistence. The "beta test" could be refugees and devastated planets living with limited surveillance and computer assistance, or perhaps the formation of the Typhon Pact, an interstellar compact existing without a virtual autocrat pulling its strings. Control could've rationalized its loss as a transformation into a meme, spreading the safety of humanity and the Federation by example rather than by subterfuge. Oddly enough, though, the Borg Invasion is also the one time Control admits failure. Maybe the destruction was too big to ignore, so while it could rationalize that it wasn't caught by surprise, it couldn't find an excuse that could justify the Invasion as a whole as something it wanted to happen.
There's also another possibility. Control and Uraei might not have the relationship we assume. Given it's Star Trek, and thinking computers seem to pop up all the time with minimal effort, it seems like the Federation would have to be constantly, actively suppressing virtually every computer network so it didn't develop an emergent consciousness. Control and Uraei could've grown up in the same system, but they might not be the same thing, or even family. Control could be something else, an emergent organism consisting of the Federation as a whole, not unlike what's described in Asimov's "The Evitable Conflict," which has choked Uraei out of the same soil.
I think I prefer the first interpretation, though. Control is gone, but it couldn't go without patting itself on the back for how cleverly it undid itself, first.
In that case, the epilogue is Control's own dying thoughts; "Yes, this is exactly what I wanted to happen from the start." Everything is going according to my plan as my mind is being eaten alive. It's really all for the best. The line about Control's "new configuration" having been in testing for five years is a bit weird, in both this reading and in the apparent interpretation. Though, the Borg Invasion was five years prior; perhaps the "new configuration" is referring to its own nonexistence. The "beta test" could be refugees and devastated planets living with limited surveillance and computer assistance, or perhaps the formation of the Typhon Pact, an interstellar compact existing without a virtual autocrat pulling its strings. Control could've rationalized its loss as a transformation into a meme, spreading the safety of humanity and the Federation by example rather than by subterfuge. Oddly enough, though, the Borg Invasion is also the one time Control admits failure. Maybe the destruction was too big to ignore, so while it could rationalize that it wasn't caught by surprise, it couldn't find an excuse that could justify the Invasion as a whole as something it wanted to happen.
There's also another possibility. Control and Uraei might not have the relationship we assume. Given it's Star Trek, and thinking computers seem to pop up all the time with minimal effort, it seems like the Federation would have to be constantly, actively suppressing virtually every computer network so it didn't develop an emergent consciousness. Control and Uraei could've grown up in the same system, but they might not be the same thing, or even family. Control could be something else, an emergent organism consisting of the Federation as a whole, not unlike what's described in Asimov's "The Evitable Conflict," which has choked Uraei out of the same soil.
I think I prefer the first interpretation, though. Control is gone, but it couldn't go without patting itself on the back for how cleverly it undid itself, first.
