A lot of this doesn't quite look like cut content, but things that changed during normal iteration processes. Like, say, Flaahgra's forest environment may have turned out too busy visually to play well, or may have been too taxing on the hardware. Ridley is in, mostly as shown. Thardus might originally have been a Magmoor boss, and all that changed was due to him being put in a different sector of the world. Omega Metroid may have been the original concept for Omega Pirate. Just like flying insectoid guy <=> jet-pack pirate.
The environment captures are recognizable as Chozo Ruins Plaza and a tunnel in Magmoor that is still in the first game. Maybe some platform moved around, yes. But they're not absent from the product as it was released.
I think it's pretty standard procedure to throw a lot of ideas around in the concepting stage, and then pick and choose the ones that seem the most promising and the most fitting. That's basically what I'm seeing in most of those examples.
Absence of Mother Brain is a bit of a bummer, yeah.