A result by Wraith and Blass states that every flat module is a filtered colimit of free modules (see nLab, Thm 1).
I am wondering if this is simply a corollary of Yoneda's density theorem which states that every presheaf is a colimit of representables, or more precisely given a presheaf $F\colon C^{op}\to \mathbf{Set}$ we have
$$F\cong colim_{(C,x)\in el(F)}Y(C)$$
where $el(F)$ is the category of elements (see nLab page) and $Y\colon C\to [C^{op},\mathbf{Set}]$ is the Yoneda embedding.
To connect these ideas, we note that the category of $R$-modules is equivalent (as additive categories) with the category of additive functors $[\mathbb{R},\mathbf{Ab}]_{add}$ where we are interpreting $\mathbb{R}$ as the additive category with one object $*$ and homset $\mathbb{R}(*,*)=R$ with obvious addition of morphisms. There is a forgetful functor
$$ U\colon [\mathbb{R},\mathbf{Ab}]_{add}\to [\mathbb{R},\mathbf{Set}]$$
which forgets the additive structures. Now if $U(N)\colon \mathbb{R}\to \mathbf{Set}$ is flat (as a functor) for a module $N$ its category of elements is filtered and we have
$$ U(N)\cong colim_{(*,n)\in(el(U(N)))}Y(*) $$
which shows that as sets we have $$ U(N)\cong colim_{(*,n)\in el(U(N)}R $$ since $Y(*)(*)=\mathbb{R}(*,*)=R$ and colimits of presheaves can be computed pointwise (which in this case is only one point $*$). Thus $N$ is a filtered colimit of the free modules of rank 1, namely $R$, as sets. We also know that the forgetful functor $G\colon \mathbf{Ab}\to \mathbf{Set}$ creates filtered colimits (all algebraic categories share this property). So shouldn't the isomorphism lift to an isomorphism of abelian groups.
An assumption I am making but am not entirely convinced of is that a module $N$ is flat iff the presheaf $U(N)\colon \mathbb{R}\to \mathbf{Set}$ is flat.
Ideally, I am looking for the answer to the following:
Can the left Kan extension $N\otimes_{\mathbb{R}}-\colon [\mathbb{R}^{op},\mathbf{Ab}]\to \mathbf{Ab}$ along the $\mathbf{Ab}$-enriched Yoneda embedding $Y\colon \mathbb{R}\to [\mathbb{R}^{op},\mathbf{Ab}]_{add}$ of a flat module $N\colon \mathbb{R}\to \mathbf{Ab}$ be computed as the left Kan extension of presheaves with values in $\mathbf{Set}$?
This is true, if I'm not wrong.
Notice that there are embeddings of $\text{Mod}_R$ and ${}_R\text{Mod}$ in the bicategory of $\bf Ab$-valued profunctors, respectively as ${\bf Prof}({\bf 1}, \mathbb R)$ and ${\bf Prof}(\mathbb R,{\bf 1})$ (in your notation, $\mathbb R$ is the ring $R$ regarded as a category).
This entails, in particular, that tensor product $\otimes_R$ of modules $M\in{}_R\text{Mod}, N\in\text{Mod}_R$ corresponds to the composition of profunctors $\star$.
This motivates the following chain of equivalences: