Suppose we have a matrix $A$. If my understanding is correct, we could see the matrix in the canonical base of a linear transformation $f$ or a bilinear form $\phi$, for example.
So, given another base $B$, we know that
\begin{align} [\phi]_B &= T^t[\phi]_ET \end{align}
\begin{align} [f]_B &= T^{-1}[f]_ET \end{align}
where $T$ is the change of basis matrix from $B$ to $E$.
As not necessarily $T^{-1}=T^t$, is the change of basis matrix characteristical of the matrix or does it really matters if we look at it whether as a linear transformation or a bilinear form?
The change of basis matrix is the same for either a linear transformation or a bilinear form. The matrix is constructed as to convert vectors whose coordinates are in $B$ back to the standard basis. This much is true in both cases.
As you indicate, however, the matrices $[\phi]_B$ or $[f]_B$ are different depending on whether you view a matrix as representing a linear transformation or a bilinear form. So in that sense it is not “intrinsic” to the matrix. This is because for a linear transformation you need to first transform into the new coordinates (apply $T$), apply the transformation, and then change back using $T^{-1}$. For a bilinear form, you need to convert both of the input vectors into the new coordinates by applying $T$ and $T^t$.
There is an important example where the $[\phi]_B$ and $[f]_B$ coincide, namely when the bases are orthonormal. In which case the change of basis matrix is orthogonal $Q^t = Q^{-1}$. Outside of this case, though $[\phi]_B$ and $[f]_B$ will in general be different.