I've already given answers to similar questions in my previous post in the thread, and I'll try to answer your ones as well, but I too haven't read the manga in many years.
I don't exactly understand the distinction you make between "human or some gene clone". We've seen the girl from the embryo in exactly one panel, head to tow in a suit and gas mask. As far as I can tell she looks human, though I guess it would be cool if this is in a way Cibo's final transformation, got to say I hadn't thought about that. Either way is possible, but I think if it was some sort of clone, Nihei would have indicated it in some way. So I'm leaning towards "ordinary" human.
My memory is muddy here, I remember the embryo being "conceived" between Cibo and Sanakan, though I may be forgetting some previous detail, like what Veldarth mentioned about Seu. Either way, in a future so far off from our understanding of time, world so alien, and technology so advanced (and rarely explained), I think this little detail isn't that unbelievable in the context of the story. Almost everything in BLAME! is a mind fuck subversion, this as well.
Again, "human" is a really murky term in the world of BLAME! Whatever her original form and her transformations actually were (and these are details that another read to refresh one's memory would probably illuminate) it won't make any real difference regarding the story or her character. I'm guessing her transformations are some sort of synthetic bodies, though with the time travel shenanigans, maybe one of her versions we see later could be her original body from a different time line or something.
The water at the end signals that Killy has actually reached the edge of the Megastructure, yes.
The girl from the embryo carries the Net Terminal Genes Killy has been searching the whole manga for, and that's the purpose she was "created" for.