You're confusing the flatness of a particular 3D hypersurface (of constant coordinate time) with flatness of 4D spacetime. The k parameter describes the curvature of that hypersurface, not the curvature of spacetime.
This is all to say that we don't live in a flat Minkowski spacetime. We live in a curved spacetime, which means that things like distance measures are much less straightforward. The curvature of 3D slices of spacetime is not the primary complication - the overall curvature of 4D spacetime (which involves the scale factor a(t)) is the primary complication.