There's a possibility as to the nature of the BETA (and the Siliconians) that doesn't get brought up enough...
So, the BETA. As far as established lore goes, they're biological mining drones - a sort of wetware version of the paperclip optimizer machine, set loose on the cosmos. They strip-mine planets for resources, which the Hives then process and launch back into space. (Try not to think about how said ballistic shipping containers are meant to actually reach somewhere they can be put to use, considering how the BETA's sphere of operation is universe-wide. Personally, I suspect G-Element FTL of some sort, but that's a different topic...)
Anyway, the main point of conflict with all this comes up when our heroes finally establish communication with the BETA Superordinate, which rejects their accusations of murder on the grounds of the inviolable principle of reality that carbon-based life is too unstable to be occur naturally, and therefore humanity must be manufactured automata like the BETA themselves - therefore, the BETA have done nothing wrong by consuming them.
Just... Stop there, for a second, and go back to the core idea of the argument: Humanity aren't people, but rather machines. Someone made them. They belong to someone - they're someone's property. And yet, for whatever reason, the Superordinate was insistant that there was nothing wrong with "recycling" them for materials and shipping them off to the possession of their Siliconian creators.
And that's where I started thinking. The line about how "carbon-based life cannot form naturally"? It's stupid. Not because it's wrong - that'd just be putting the logic backwards - but because it's uneducated. Even we - humanity, barely interplanetary in reach, nowhere even close to extrasolar capabilities - have the scientific knowledge to recognize the inverse; that silicone-based life, as improbable as it might be by our own anthropocentric criteria for the requirements of life, would still have the possibility of occurring naturally. And the Siliconians? Galaxy-wide reach and scale, bioengineering like we could never even dream of, synthetic elements that violate the laws of physics as we know them - they know more than us.
So, the BETA's Siliconian creators saw nothing wrong with them "recycling" other people's hardware. The "carbon cannot be people" line that they use to judge what they can and can't consume is bullshit, and they know it. The raw materials they harvest are processed into synthetic G-Elements that violate the laws of physics as we know them - even proving capable of facilitating access to, alteration, and even destruction of entire realities outside their original source. And, assuming that the Superordinate's claim as to their being 10^37 BETA in existence refers to other Superordinates rather than regular strains, they've already been deployed to nearly every star in the observable universe.
My first conclusion: The carbon-based-life principle is a deliberate falsehood. Suppose a bunch of humans made some autonomous, self-replicating mining drones, to be thrown out into the universe to send back a steady supply of resources. In the face of the obvious complaints of "What's keeping them from turning into a godless horde of flesh-eating murderbots that consume any poor alien civilization they stumble upon?" the creators simply respond, "Ah, but you see - we programmed them to NEVER consume carbon-based lifeforms. And as we ALL KNOW, any sort of biological lifeform - and any intelligent species that could evolve from them - could ONLY come from carbon-based biology!" Now, keep in mind that "carbon-based life" is a scientific concept. "Life might be able to evolve outside of a carbon-based structure" is a higher, and murkier scientific concept. And remember the fact that the average Joe on the street, the people that make up the overwhelming bulk of our civilization, have very little scientific education or understanding. At the first sign of conflict, the "obvious scientific principle" gets taken as religious dogma, because while nobody understands it properly, it's still relatively closer to their own knoweldge base than a more complicated and far less certain scientific possibility, which is simply discarded. The Siliconians are no different - some scientists might admit the possibility of carbon-based biology, the majority of their scientists recognize the primacy of silicone-based lifeforms - so the bulk of their civilians disregard the first as crackpot pseudoscience, latch onto the second as fundemental fact, and the BETA's "creators" get the plausible deniability they need to let their murderbots dig into the universal buffet.
My second conclusion: Whatever the "creators" are after, whatever the Hives keep shooting off into dark space - they really need it. They've dispatched the BETA to strip mine planets across the entire universe just to get enough of it. The supply shipments have to carry some form of self-propulsion - the fastest object to ever be shot out of our own atmosphere did it at 67 kilometers per second, which means that the Big Crunch will have arrived before it even makes it halfway across the universe - and considering what we know about G-Elements, some kind of FTL capability isn't just possible, but also highly likely. Speaking of G-Elements, the fact that the BETA's mining operations cover so much of the universe suggest that they can be made from just about anything - therefore, if G-Elements are the product being sent back home, then the problem that the BETA are meant to adress isn't availability; it's scale. For whatever reason, the Siliconian creators decided they needed to exploit the untapped G-Element production resources of the entire universe. Remember, the G-Elements of a small part of a single planet, harnessed and exploited by the broken mind of a child, were enough to shatter realities just to fulfil her desperate and disjointed yearning. Considering this, when you look at the scope of the BETA's resource extraction, you have to ask: What the hell could an entire species do with a UNIVERSE'S worth of G-Elements?
Now, my third and final conclusion, where I start to make shit up: The Siliconians who made the BETA, did so to let them escape. There's this kinda old story, one that was forgotten by all but a loyal few, only to be remembered by more as of late, about a machine that sought to live forever; the only problem with all that is that the universe itself isn't very conductive to eternal existence - even if its own existence is not finite, it still lives in constant cycles of expansion, contraction, total collapse into a singular point, and then explosion out of that singularity into a reborn universe. All well and dandy for reality, unless you happen to be something inside said reality when everything goes crunch. If you want to live forever, you need to be able to leave, to step sideways into another universe not currently suffering from exponentially decreasing headroom - not just once, because whatever new universe you find will still suffer the same fate sooner or later, but again, and again, and again, every time that time runs out. That is the ONLY WAY you can maintain the absolute security of your own existence. We've already known this for years. The Siliconians have known this for far longer. And we all know that G-Elements, if properly utilized, can breach the barrier between realities. Consider the likely scale of the G-Element resoures that were used throughout Muv-Luv, where only a single individual did any sort of reality-hopping. Now, scale that shit up to the kind of civilization that can cover an entire universe with their creations. And keep in mind the critical phrase here: A universe. Not "the" universe. Because if the Siliconians did make the BETA to enable them to escape the big crunch, and the scale of their civilization is large enough that it requires the strip mining of the entire universe to produce enough G-Elements to fuel the process, then what's to say that this isn't the first time that they've escaped? How many universes have they left behind, strip-mined into lifeless husks to feed their eternal getaway act? How many more universes will they do the same to?