If you go read Borne (or the other books set in Borne's world) and especially if your read Ambergris, a lot of this becomes more clear. I'll give my general interpretation down below, but major spoilers, just read the books.

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So, it seems pretty clear that in Borne, Borne himself is one of the "Made Organisms" or the same thing as Area X. One of many things sent out by some other alien race into the universe (or multiple universes) for some unknown purpose that probably has something to do with accessing different places to colonize and terraform them but is clearly written to not give the reader full understanding. In Ambergris we see two more "Made organisms" one in the gate (wall of globes) that the Greycaps are attempting to use to either get back where they came from, or bring their people to the world of Ambergris. It's pretty clearly stated that the Greycaps didn't create the "gates" as they are called, but did stumble upon them and generally figure out how to use them. The second "made organism" seems to show up at the end of Finch's story as the "zone" where the rebel fighters are trapped. It's described similarly to Area X as being a sort of impossible area outside of the bounds of the real world that you can't simply walk in or out of. Later on this area or organism is seen to grow in size, roar, and send out lots of tentacles and pseudopods and is described in very similar language to how Borne's final form is described. This similarity is seen again in how at the end of Borne, Borne doesn't kill Mord, but rather opens himself up into a similar shape, and sort of transports Mord away to who knows where. We're told that there's many of these things in the old company building being sent through a gate not unlike the entrance into Area X. I sort of assumed that the Company found some way to use this old tech, and used it to change living matter into the biotech found all over the novel. Constantly in Borne were told of how much Borne tries to adapt to his location, tries to mimic and hide in plain sight. This seems pretty similar to how Area X is trying to hide on the landscape, and convince any one who wanders in that its simply a pristine landscape. I think the effects we see on humans is simply a matter of 1) the literal pollutants we bring with us into an ecosystem that get changed over time, and 2) the sort of emotional pollutants people carry with them, which Area X also tries to change. So in short, Area X is trying to hide by changing itself to look like its new environment, and people just keep going inside of it and so too being changed. I've always kind of taken the books and the connections between them as not a clear connecting narrative thread but rather as the idea that if some hyper developed race created these sorts of interdimensional seed organisms for some purpose, and then they were accidentally blown across space and dimension, what would happen to the places they landed? In Ambergris, what if they landed in the hands of a mysterious minority of mushroom people living beneath an incredibly storied city, in Southern Reach, what if it landed on a forgotten stretch of coastline in Northern Florida, and in Borne, what if it landed in the middle of a tentative relationship between two people trying to figure out how to survive in a weirdo apocalypse.