As for B-weapons, these are highly specialized organisms to work under a very specific situation. Bacterias that are able to thrive within us, inside of a closed wet etc organic body will ususally die when brought to a different habitat like a clean, dry, cool metallic surface in exposure to aggresive agents like oxygen and certain EM waves. And a bacteria that would metabolise metal wouldn't be able to metabolise anything inside of an organic body. It's not like a bacteria is a sort of a sentient being that has a toolbox & a second set of clothing with it to adapt to new surroundings. Or a virus, this is even more specialized, it cannot even replicate on its own, it needs other cells to do it for it, which is something a crystaline metal structure can't do for it.
Irrelevant. If you are genetically modifying the organism, you can specialize it to the point where it attacks metal preferentially. We're working on a nano-scale at this point. 'Organic' is just carbon compared to silicon at the scale we're looking at. IF you insist that biologicals must be organic (which they really don't, as it's arguable just how alive some micro-orgnisms are - prions, for example, are basically just lumps of protein), then we already have examples of naturally-occurring, unmanipulated bacteria which eat metals quoted within the thread. There's no reason whatsoever that couldn't be weaponized, accelerated and adapted, even with present-day GE technology. And if we include nanobots into the biological category (as many nano-bots are basically constructed from biological materials), then a very fast-acting, silicon-based, self-replicating grey-goo machine would be able to reduce the population of whole planets to dust in a matter of hours, before the Yor have a chance to quickly refit themselves.
Maybe my understanding of how a robotic lifeform works is different than yours. Unlike they us their bodys aren't bound by DNA, it's mostly entirely mechanical, meaning they can rip it off and replace with just anything. From brings alot of advantages to the table. I deduce that from their ability to factorize their population. If they start colonizing a planet which holds a possible danger to their bodily structure they simply choose a better outfit. It's more or less like adapting a car to sell either in Siberia or Arabia. The only thing they possibly can't change is the module holding the Spark of Life, which gives them sentience, and which has been stated lorewise that they can't manipulate it as they don't full understand how it works (see eg range techs "Cybernetic Life Support" in GC2).
No, that's how we see it too - it's just that this isn't actually that different to organics. Just as the Yor might adapt to make themselves immune to the latest anti-robotic biological organism, we immunize and vaccinate. I'd assume that the 'biological weapons' in question are in constant development, as are defences against them; the initial tech cost is the basic research needed to create and tailor a wide range of offensive weaponized biological agents more or less at will with next to no cost - the computer to manipulate the genome, rather than the manipulation process itself.
But the Yor have been known to be immune to attacks on that level as they got Firewalls & Antivirus Software as techs baseline otherwise the implications would be there to attack them at that level, which could probably kill the whole civ by one command, or make them all slaves etc, which would mean a I-win-button or 1-shot-kill mechanism, which, either way, is not a good mechanism for a strategy game. But I would agree if theirs a tech introduced to specifically work only against cybernetic lifeforms but not against organics, one thing that already works nowadays are EMPs.
Firewalls aren't impervious, and even heuristic anti-virus software needs to be updated regularly. Once again, as long as the Yor are aware of a particular computer-type attack then they will undoubtedly move to counter it, just as the squishier races presumably feel the need to produce anti-toxins and targeted antibiotics in response to new biological attack vectors. I expect that the Yor do have some means to isolate or shut down whole areas of their network that are infected with APTs; indeed, personality-wise, the Yor response to an aggressive, fast-spreading computerized assault on their primary operating systems is probably just remorselessly isolating and kill all units which have contracted it rather than saving them in some way. That may be entire planetary populations burning their modems and waiting for death.
And yes, I don't like techs like "Doom Ray" to me that's infantile and poor. Especially that, within theoretical quantum physics, there are so many particles we already know that they exist for real, just that we can't use/manipulate them nowadays on a larger scale mostly because the energy requirements are too severe. But that should be something that could be remedied in a few hundred years, why not, esp. that the techs in GalCiv states there's controled fusion reactors and artifical gravity. So even using only theoretical physical concepts like the graviton, gravitino, strings or quantum looped fabric of space etc pp is still better than stuff like (from GalCiv1, writing from memory) Galaxy Generation "We now can make new galaxies, it's not that hard once we've figured out how to do it but sadly the range is very limited. And as one scientists stated, it's not a good idea to create a galaxy right inside of another galaxy, so the use is mostly military related"
(that tech didn't do anything, but I think you get it that it's not really immersive, at best it tried to convey some humour)
But galaxy generation simply implies a massively higher level of control over the laws of physics than we presently command. Galaxies generate over time. Therefore, the rules to create galaxies exist in physics. So we just need to know how to accelerate the process. If gravity generation can be achieved, then it can be done on a massive scale (eventually), which means that you can collect the matter rapidly into one place. Then you just ignite a few pockets of hydrogen to make some suns (rather than waiting for them to do so themselves), and the whole process goes by itself from there - though obviously you can continue to adjust by that point, using field manipulation to shunt vast quantities of atoms together and subjecting them to pressure until they form planets etc. None of this is outlandish fantasy stuff.
By the end game, you are on the edge of transcending physical reality completely and reaching a higher state of consciousness. You're operating in 11 dimensions. Bending the laws of physics should be fairly trivial at the remove. Moreover, the fundamental particle which we play around with presently are a distant memory; science has moved on and there's been paradigm shift after paradigm shift. The cutting edge of the Standard Model is a quaint artifact of history at that stage, like Pholgiston or Ether; quantum physics and relativity have long since settled their differences and been replaced with the Theory of Everything. 'Doom Ray' is as good a description as any, since frankly we have no idea what the physicists of 2400AD will be talking about - but we can be pretty sure it won't be quarks and M-branes. Half the comedy of the research screen descriptions comes from the fact that these are insanely highly-trained scientists trying to explain what their working on to someone who knows so little science from their point of view that you don't even know the name of the forces that they're manipulating. It would be like trying to discuss the workings of an atom bomb to a medieval peasant.