I see two similar but distinct techniques at play in Wanix: "everything is X" and "X is a useful representation for many things". The first is about implementation, the second about interfaces.
In Wanix, it is not true that everything is a file. The DOM certainly isn't, as you modify it from JS outside of Wanix. The VFS simply provide a file view to it. On the other hand, every service is a capability, by implementation, and there is no way around it.