I do not know the warp as you do,’ said Yesugei. ‘But I know is not that simple. Otherwise, no movement is possible at all.’ ‘There are layers,’ said Veil, impatiently. ‘Yes, there is stratum aetheris, the shallow ways.
This is the region where the Astronomicon shines and you can use it to navigate these region. I really think 'Stratum' here is describing a 'region of layers' as opposed to a single layer.
There is stratum profundis, the greater arteries, plunging deeper.
This is the largest region of the warp where the majority of the Realms of the Gods of Order and Daemons of Chaos would reside.
There is stratum obscurus, the root of the terror.
Here there is no protection of the Astronomicon, all lights go out and the Realms of the Chaos Gods begin
How does this help you? No living man can navigate the deep ways. Even he could not.’ ‘But you try to map it.’ ‘It could not be done.’ Veil shook his head with frustration. ‘He was wrong about that, at least. It is not a mirror. It moves like a living thing. It is a living thing. Touch it, and it trembles.’ He briefly lost his certainty. ‘I do not have the Eye, but still I have seen things. I have studied what they study. The complexity is… immortal.’ ‘Try to explain.’ Yesugei spoke softly. ‘I am fast learner.’ Veil exhaled, his eyes widening. ‘The Seethe is an ocean. All know this – it has currents, it has depths, it has storms. Near the surface, you can see the Cartomancer’s light. You can follow it. You can use your Geller aegis, and you are kept barred from the Intelligences. But even then, you are just below the upper limits. Go deeper and the aegis shatters. The lights go out. The Eye is blinded. When men say that they traverse the warp, they boast, for no mortal does more than skim across eternity’s face, like stones thrown by a child. We do not belong there. It is poison for us, and the deeper in, the worse the poison.
Here he goes into more detail about the Stratum obscurus or the region beyond the Cartomancers light.
I really think he is referring to regions of the warp as defined by the Astronomicon as opposed to describing the actual layers themselves which would also fit in the definiton of 'Stratum' as describing a 'region of layers' or a layer itself.