I cannot say much about the $\ell$-adic side.
I will give "classical" answers to 1)-3):As you know, the Riemann-Hilbert correspondence says that on a smooth complex variety $X$ the category of $A$ of vector bundles with flat regular singular connection is equivalent to the category of representations of the topological fundamental group $\pi_1^{\text{top}}$ on finite dimensional complex vector spaces. Lets write this category $\operatorname{Repf}_{\mathbb{C}} \pi_1^{\text{top}}(X)$ (neglecting base points).

Since $\pi_1^{\operatorname{et}}(X)$ is the profinite completion of the abstract group $\pi_1^{\operatorname{top}}(X)$, a representation of $\pi_1^{\operatorname{top}}(X)\rightarrow GL(V)$ which factors through a finite quotient can be thought of a representation of $\pi_1^{\operatorname{et}}(X)\rightarrow GL(V)$ which is continuous with respect to the profinite topology on the left and the discrete topology on the right. Hence, given an etale covering of $f:Y\rightarrow X$, Galois theory associates with it a finite $\pi^{\operatorname{et}}(X)$-set, which we can linearize to and get a representation and then a $\mathcal{D}$-module. But what does this mean concretely? It is not difficult to check that ${f_*}\mathcal{O}_Y$ is a $\mathcal{O}_{X}$-coherent $\mathcal{D}_X$-module (hence a vector bundle), and it is a theorem that it is regular singular (Gauss-Manin).

About your third question: The pro-algebraic affine group scheme associated with the Tannaka category $\operatorname{Repf}_{\mathbb{C}} \pi_1^{\operatorname{top}}(X)$ is by definition the pro-algebraic completion of the finitely generated group $\pi_1^{\operatorname{top}}(X)$. The etale fundamental group is the profinite completion of this group. And amazingly, the profinite completion "controls" the pro-algebraic completion:

**Theorem**: Let $f:G\rightarrow H$ be a morphism of finitely generated (abstract) groups. Then $f$ induces an isomorphism on pro-algebraic completions if and only if it induces an isomorphism on profinite completions.

I am told that this was first discovered by Malcev, and then independently rediscovered by Grothendieck. Grothendieck precisely had the application the the Riemann-Hilbert correspondence in mind.

See: Grothendieck, Alexander
Représentations linéaires et compactification profinie des groupes discrets. (French. English summary)
Manuscripta Math. 2 1970 375–396.