I'll expand a bit on the relationship between naturality and independence on the choice of basis.
The connection is most obvious when looking at natural transformation $η : \mathrm{Id} ⇒ \mathrm{Id}$. In that case, naturality means that for every $A : V → W$ we have $η_WA = Aη_V$.
Notice first that a choice of basis for $V$ is the same thing as an isomorphism $E : ℝ^n → V$, and given an operator $A : V → W$ and a basis $F : ℝ^m → W$, $F^{-1}AE : ℝ^n → ℝ^m$ is exactly the matrix of the operator $A$ in the given pair of bases, under the canonical identification of $L(R^n, R^m)$ and $M_{mn}$.
Now by applying the naturality condition of $η$ to a choice of basis $E : ℝ^n → V$, you get that $η_VE = Eη_{ℝ^n}$, and consequently $η_{ℝ^n} = E^{-1}η_VE$. This literally says that the matrix of $η_V$ is equal to (the matrix of) $η_{ℝ^n}$ in every basis $E$ of $V$ (which incidentally means that $η$ has to equal $rI$ for $r ∈ ℝ)$.
In your case you have $η : V → V^{**}$, which means that to talk about coordinate independence you need bases for both $V$ and $V^{**}$, and you can't ask for $η$ to be the same for an arbitrary choice of these bases. It doesn't make sense intuitively because you still want the entire thing to only depend on the choice of basis for $V$, and it would force $η$ to be $0$ anyway.
Fortunately, by the functoriality of $(-)^{**}$ a choice of basis $E$ induces a choice of basis $E' = (ℝ^n ≅ (ℝ^n)^{**} \stackrel{E^{**}}{\longrightarrow} V^{**})$ for $V^{**}$, and we have that $η_V$ always looks the same in any pair of bases $(E, E')$ (it's the identity matrix if you choose the canonical isomorphism for $ℝ^n ≅ (ℝ^n)^{**}$), so $η$ is again coordinate independent in the appropriate (and only reasonable, really) sense.
In general this talk about bases becomes cumbersome, and it's better to think about automorphisms $φ : V → V$ directly as changes of coordinates on $V$, or symmetries of $V$. Then you can just think of natural morphisms $η : FX → GX$ as of being invariant under the change of coordinates $(Fφ, Gφ)$ of the pair $(FX, GX)$, which is induced by the change of coordinates of the base object $X$, which makes the slogan that natural transformations don't depend on the choice of coordinates formally true.
Just keep in mind that the converse isn't true. Not every transformation between functors that is coordinate independent in the sense above is natural, because coordinate independence only gives you naturality squares for isomorphisms, and not for every morphism in the category.