Substrata most definitely falls under the category of 'ambient music'. However, my own experience with the album has left me with quite a different impression.
Whenever I listen to 'Soundtracks for the Blind' by Swans, I find myself being emotionally drained as the album progresses, like my soul is being slowly sucked out of me over the course of 140 minutes. By the end, I find myself quite emotionally exhausted and need to take a bit of a break before listening to something else. It's very much a credit to the album that it's able to elicit this kind of response in me, the tracks are simply capable of pressing emotional buttons that other artists cannot. I'm mentioning this because a similar thing occurs when I listen to Substrata.
This comparison between Swans and Biosphere is somewhat interesting, as, while Soundtracks for the Blind definitely strays into 'ambient' or 'quiet' territory from time to time, a lot of the album is quite loud. This doesn't happen in Substrata. Biosphere seem determined to keep their noise level firmly bounded from above and, as a result, climaxes or resolutions to the musical build-ups never occur; that's if the build-ups even exist. Maybe this is why I find myself slightly unsettled when I listen to this. We've gotten so used to bands like Explosions in the Sky and what not delivering us long-winded build-ups and explosive peaks that, when this structure is taken away from us, it sounds quite different and almost upsetting. By keeping its volume low, there's always a sinister feeling to the album, as if it wants to scream at you but knows it would be pointless to do so and, instead, keeps it anger brooding but partially hidden.
Of course, it takes more than just a quiet album to give off these feelings of unease (I could, after all, just play any album with the volume low). Where Substrata initially conjures its unsettling atmosphere is in its chord progression and use of samples. The chord progression, while firmly rooted in minor keys, is quite unique and, a lot of the time, does not exactly sound "nice"; nor should it. The samples, usually of various nature sounds and people talking, contrast each other nicely, with the nature sounds providing some relaxation whereas the voice samples complement the unsettling atmosphere of the music perfectly.
In this post, I've tried to explain why I find Substrata quite an emotionally involved album. I doubt I did it very well, but the point is that it affected me quite a lot. Even after 15+ plays I still find it an unnerving listen. While I will happily call this an 'ambient' album, all the signs are there after all (drone loops, quiet texture etc.), I find the idea somewhat ironic as the whole point of ambient is that it's not supposed to be too distracting. However, if I'm listening to music whilst doing work or something, I have a better chance of being able to focus on my work (and not the music) by putting on Merzbow than I do by putting on Substrata. I'm not kidding.