I think this is clearest in the Normalizing Flow cases because you're just turning your space into a Gaussian (diffusion does this too, but through approximation methods and isn't invertible, though it is reversible). You project the image/sentence/data you want to manipulate, manipulate within gaussian space, then return back to target space.
Or maybe my confusion is shared confusion because embedding is an overloaded word that means a lot of things? Maybe you're just thinking of the first block that converts discrete integer tokens into continuous floats? But we learn those embeddings so even though it becomes like a lookup table it's still a neural process. People do things like SVMs on this space alone. But I think it is like latent space, which is only a bit more abstract. At least embeddings need to be injective, well... mathematically...