You're dealing with different geometric objects: Tangent vectors, which can be realized as equivalence classes of curves, and cotangent vectors, which can be realized as equivalence classes of real-valued functions (think differentials).
There's a natural linear pairing operation between these objects: Compose a curve and a function, and you get a map $\mathbb R\to\mathbb R$. Take it's derivative at the point in question, et voilà. This pairing operation allows us to consider the spaces as 'dual', and in particular identify the cotangent space with the space of linear functionals on the tangent space.
Given a coordinate system on a manifold, the coordinate lines are curves, yielding a basis of the tangent space, whereas the components of the coordinate chart are functions, yielding a basis of the cotangent space. It's easy to show that these bases are algebraically dual, ie their pairing yields the Kronecker delta.
On (pseudo-)Riemannian manifolds, there's additionally a metric tensor $g$, a non-degenerate bilinear form. This tensor induces an isomorphism $g^\flat:v\mapsto g(v,\cdot)$ from the tangent to the cotangent space ('lowering the index'), with an inverse map $g^\sharp$ ('raising the index').
The map $g^\sharp$ can be used to pull back our basis of the cotangent space onto the tangent space, yielding the reciprocal basis. The components of a vector $v$ relative to the reciprocal basis of the tangent space are the same as the components of the covector $g^\flat v$ relative to the dual basis of the cotangent space. This makes it possible to conflate vectors and covectors, but that's considered a mostly bad idea nowadays.
Having said all that, now on to your actual question:
But if I were to take a vector $V^{\mu}$ and lower the index to a covector $V_{\mu}$ in flat space, it most certainly would not be the complicated change of basis matrix shown in the example. Am I missing something here?
The Minkowski metric is that 'complicated change of basis matrix' - it's just that you're dealing with an orthonormal basis, which makes it simple.