I believe the confusion lies in a common abuse of notation of denoting by the same symbol the $(1,1)$ tensor and the associated linear operator. Let $A:V\to V$ be a linear operator on the vector space $V$. Define the following $(1,1)$ tensor $\widetilde{A}:V\times V^\ast \to \mathbb{K}$, where $\mathbb{K}$ is the underlying field of scalars,
$$\widetilde{A}(v,\phi)=\phi(Av)\tag{1}.$$
In this scenario we started with some linear operator $A$. Given that, we know how to evaluate $Av$ for any $v\in V$. Therefore we know how to evaluate $\phi(Av)$ for any $\phi\in V^\ast$. So we have everything we need to evaluate (1) for any pair $(v,\phi)\in V\times V^\ast$. That this is a multilinear map can be easily checked.
This establishes a linear map ${\cal I}:{\rm End}(V)\to T^1_1(V)$ where ${\rm End}(V)$ is the space of linear operators in $V$ and $T^1_1(V)$ the space of $(1,1)$ tensors in $V$. The map is just ${\cal I}(A)=\tilde{A}$.
Now we would like to find its inverse. To do so we rewrite (1) in a convenient way. Recall that covectors are defined to be linear functionals $\phi:V\to \mathbb{K}$, in that case they naturally act on vectors $v\mapsto \phi(v)$. The thing is that if you fix a vector $v$ and define $\Phi(v):V^\ast\to \mathbb{K}$ as $\Phi(v)(\phi)=\phi(v)$ then the map $\Phi(v)$ is a linear functional on $V^\ast$. This is just to say that we can either view $\phi(v)$ as $\phi$ acting on $v$ or as $v$ acting on $\phi$. In fact, in some texts authors even write this as $\langle \phi,v\rangle$ to notationally emphasize this point.
So look to (1) and, instead of viewing it as the action of $\phi$ on $Av$, look at it as the action of $Av$ on $\phi$. In other words, using the map $\Phi$ we defined
$$\widetilde{A}(v,\phi)=\Phi(Av)(\phi)\tag{2}.$$
Since this is valid for any $\phi$ we are left with an equality of maps $V^\ast \to \mathbb{K}$:
$$\widetilde{A}(v,\cdot )=\Phi(Av)\tag{3}.$$
Now observe that this $\Phi$ is a map $\Phi:V\to (V^{\ast})^\ast$. In finite-dimensional vector spaces one may show that this map is a linear isomorphism. In that case, applying its inverse $\Phi^{-1}$ to the above equation one obtains $Av$ starting with $\widetilde{A}$:
$$Av = \Phi^{-1}(\widetilde{A}(v,\cdot))\tag{4}.$$
This defines ${\cal I}^{-1}:T^1_1(V)\to {\rm End}(V)$. All this abstract story, however, can be written in components, so let us do so. Let $\{e_a\}$ be a basis of $V$ and $\{\omega^a\}$ be the dual basis of $V^\ast$. Start with $A:V\to V$. This operator is defined by its components in the basis, $A e_a = A_a^{\phantom a b}e_b$. Likewise, a $(1,1)$ tensor $\widetilde{A}$ is also defined by its components:
$$\widetilde{A}(v,\phi)=\widetilde{A}(v^ae_a,\phi_b\omega^b)=v^a\phi_b \widetilde{A}(e_a,\omega^b)=v^a \phi_b \widetilde{A}_{a}^{\phantom{a}b},\quad \widetilde{A}_{a}^{\phantom{a}b}=\widetilde{A}(e_a,\omega^b)\tag{5}.$$
Given $A$ we construct $\widetilde{A}$ following (1). Its components are:
$$\widetilde{A}_a^{\phantom{a}b}=\widetilde{A}(e_a,\omega^b)=\omega^b(Ae_a)=\omega^b(A_a^{\phantom{a}c}e_c)=A_a^{\phantom{a}c}\omega^b(e_c)=A_a^{\phantom{a}c}\delta^b_{\phantom{b}c}=A_a^{\phantom{a}b}\tag{6}$$
so we see the components are exactly the same. Obviously had we started with $\widetilde{A}$ and constructed $A$ following (4) the result would be the same since we have already argued that (4) construction gives exactly the inverse of the map defined in (1) we studied above.
So in the end of the day, droping notational distinction between $A$ and $\widetilde{A}$ is an abuse of notation, very common in Physics, motivated by the fact that the two objects are related by a linear isomorphism and, in particular, that they have exactly the same components when one works in terms of components (which is also very common in Physics). From the Linear Algebra perspecive, though, it is important to understand that what is really going on is what is described above. So my advice is this: know when something is an abuse of notation, learn to get used to it, but make sure you understand what is actually happening behind it.