Headscratchers / Knights of Sidonia

• Why is Kunato never revealed to have Ordered Tanikaze to detonate his explosives early during the battle with the Gauna pod? While Nagate is a dense guy, even he would most likely let someone know that he was told to detonate. Sure, it would only be testimony that people who question, but I sincerely doubt that the Gardes don’t have mission recorders/black boxes to record information from battles. If the Tsugomori or Kunato’s Garde were examined and the data from those recorders pulled, it would be enough to prove Nagate’s innocence. And yet, that doesn’t happen. Nagate never defends himself (probably out of guilt for being the cause of so many pilots, including Hoshijiro), and no one ever finds out what happens. The anime says something about the logs being classified, but the fact that they are in the first place is VERY suspicious, even if they are recordings from a military operation (which is still suspicious considering that there are other recording that aren’t, given that pilots can watch live feeds during missions. What’s the deal?
• How on Earth does the Sidonia have enough genetic diversity to have a viable population, especially given that all but 400 people were killed by Gauna centuries ago? Sure, they can do some ridiculous feats of genetic engineering, given the whole human photosynthesis thing not to mention the immortality that Nagate has from being a modified clone, but you can only twist and alter DNA so much, right? Especially when you’re already messing with cloning.
  • The biggest problems with starting with a low population are that A. Inbreeding promotes the expression of latent genetic defects, and B. Lack of diversity of traits which will benefit in later adaption. I can't imagine the first being an issue with their level of genetic engineering technology (and social control). The second only matters once they start colonizing a world, since there's no need to (genetically) adapt in their static environment. Anyways, if they can add photosynthesis and biological immortality into the genome, I'm sure they can push needed adaptions onto the population without natural selection. (This brings up a new problem, which is that controlled adaption could slowly eliminate natural diversity altogether, but that's more of a social "world of clones" issue than a survival one.)
• How the hell does the whole “third gender” thing work? More specifically, how does a human body completely alter its structure to transform from something that isn’t male or female into something that IS? The sheer amount of reconstruction of the skeletal system alone is insane, not to mention growing/losing ovaries, developing gonads and a penis…..honestly, I think that’s more of a wonder of genetic engineering than the photosynthetic humans…..