Let $R$ be a Commutative Noetherian ring, let $\mod (R)$ be the category of finitely generated $R$-modules. Let $\mathcal C \subseteq \mod(R)$ be an $R$-linear (https://stacks.math.columbia.edu/tag/09MI ) additive category.
Let $F: \mathcal C \to \mod(R)$ be a covariant $R$-linear functor such that $F(M)\cong M, \forall M \in \mathcal C.$ Let $i_M : \mathcal C \to \mod(R)$ be the inclusion functor that takes every module (and every $R$-linear map between modules ) in $\mathcal C$ to itself.
My question is: Is the functor $F$ naturally Isomorphic to $i_M$?
Here is a variant of Stahl's example that shows the answer can be no even with significantly stronger hypotheses that avoid examples that might seem overly degenerate. In particular, the answer can be no even if $\mathcal{C}$ is a full subcategory and $F$ is fully faithful.
Let $k$ be a field and let $R=k[x,y]$. Let $I$ denote the ideal $(x,y)\subset R$. Let $\mathcal{C}$ be the full subcategory of $\mathtt{Mod}_R$ consisting of all modules that are a finite direct sum of copies of $I$ and $R/I$. Note that $\operatorname{Hom}(I,I)=R$, $\operatorname{Hom}(R/I,R/I)=R/I$, $\operatorname{Hom}(R/I,I)=0$, and $\operatorname{Hom}(I,R/I)=(R/I)^2$ (since we can independently map each of $x$ and $y$ to any element of $R/I$). Now define a functor $F:\mathcal{C}\to\mathtt{Mod}_R$ which is the identity on objects as follows. On morphisms among $I$ and $R/I$, $F$ is the identity on $\operatorname{Hom}(I,I)$ and $\operatorname{Hom}(R/I,R/I)$ but swaps the two coordinates of $\operatorname{Hom}(I,R/I)=(R/I)^2$. This preserves composition, since the only nontrivial compositions just correspond to the $R$-module structure on $\operatorname{Hom}(I,R/I)=(R/I)^2$ and the swap map is $R$-linear. Then you extend $F$ to morphisms between direct sums of $I$ and $R/I$ in the obvious way so that it is additive.
To see that $F$ is not naturally isomorphic to the inclusion, just note that the swap map on $\operatorname{Hom}(I,R/I)=(R/I)^2$ cannot be turned into the identity by composing with isomorphisms $I\to I$ and $R/I\to R/I$ (since any such isomorphisms are just multiplication by some element of $R$).