Chern-Simons theory has action $$\tag{1} S = \frac{k}{4\pi}\int_X tr(A\wedge dA + \frac{2}{3}A\wedge A\wedge A).$$
Here, $X$ is some compact 3-manifold, perhaps with boundary, and $A$ is a connection 1-form on a principal $G$-bundle for some compact Lie group $G$.
At first glance, the theory seems to be topological, for the simple reason that no background metric appears in the action. But I have two doubts about this (which may well be related, hence my including them both in the same question):
It is standard (e.g. see p3 of Elitzur et al) to split $A$ into "spatial" components $A_i$ and a "timelike" component $A_0$. Then the equation of motion for $A_0$ leads to the constraint $F_{ij}=0$ -- that is, the spatial components of the curvature vanish. But the $F_{0i}$ components are unconstrained. So there's an asymmetry between the "space" and "time" directions, which should be identical as far as topology is concerned.
Chern-Simons on a manifold-with-boundary is supposed to be dual to a chiral WZW theory on the boundary. The WZW theory is a CFT: it is defined on some background conformal structure. But if Chern-Simons is truly topological, where does the necessary conformal structure on the boundary come from?
So, is Chern-Simons really a topological theory? And if not, where does the extra geometric structure come from?