The action of Chern-Simons theory on a 3-manifold M3 can be written as a boundary term of Yang-Mills theory on a 4-manifold M4 of boundary M3. If one is interested in M3=R3 then a natural choice is to take M4 to be a four dimensional half space R+×R3 of boundary {0}×R3. Strictly speaking, R4 has no boundary (at least in the most naive sense) and so writing things like ∂R4 is not really correct if no additional precision is given.
To ignore boundary terms is only reasonable in some cases (when they are none or when their contributions obviously vanish). Chern-Simons theory is a natural theory living on some 3-dimensional boundary of 4-dimensional Yang-Mills theory. One can define and study Chern-Simons theory independently of this fact but to remember this often sheds light on important issues (example: quantization of the Chern-Simons level is related to the quantization of the instanton number).