Well, I'd say that in this particular we can have a reasonable debate or difference, slightly divergent variations following from that seeming "defeat". I am cautious about that particular word for it is such a human one... but still even accepting it, I thnk all readings are only retroactively true, that is, only by assessing what happens next in this world can we classify what happens in FS2. This is the place of prophets or (amazing) politicians, those who are able to
create events as narratives. This is what Bosch did in his own style, but there could be other readings far less bloody and far more positive.
We could read the events of FS2 as part of the human species' awakening to the harsh reality of its temporal condition in the universe (just as a person reaching his middle age grasping more and more his own mortality for what it is), we could dissect this as a positive trait or a negative one, I mean,
everything eventually dies, it's how we deal with this truth that can be either a defeat or a victory. It could be written like the movie "Melancholia". It could be written both ways. We could read them as just a very harsh lesson, one which mankind could eventually adapt to and overcome some eons later. It could be written in "Childhood's End" style, that is, mankind is over but it births something of value to the rest of the universe. It could be written as "the cutesy species known as mankind and vasudankind, desperate for a solution for the shivan problem, end up creating a monster even greater, worse than anything created before", which would be (I guess), the "Mass Effect idea" but done right.
Everything is open in FS2 and I appreciate it a lot. Despite the harsh words I used against Lorric's rendering of the "shivans fold" idea, I agree that it could eventually work if the writing was extremely solid. It's the kind of idea so ridiculous that it could crash the entire story if done less than perfect.
So... You're basically saying that BP has the most likely story, that takes everything into account and without actually using the wording, you are suggesting that BP's theory is best. Perhaps let Darius or Axem do the BP publicity because it might make me want to hate it less due to arrogance... 
Don't get me wrong. I have enjoyed what I've played of BP. I just think its awefully pompous to pop into a thread full of people's ideas and imaginings of their favorite space Sim and suggest that your mod is the only one that really got it right. That none of the others really matter. It's that interview thread all over again.
I read it in two ways, both as just corny HEY LOOK AT ME IM AWESOME typical Battuta's style, that is, not to be taken seriously at all, and also as being just truthful. I mean, yes, we have quite a lot of post capella mods, but which ones have really dealt with this question at all? And in all of those, which ones have garnered any slight interesting theoretical development of what the Shivans are, what they should be, what is this all about and so on? The only mod that gave me pause before BP was "Sync", but its commentary was minimal.