In the following, an algebraic stack means a stack over the big fppf site of a scheme, admitting a smooth, representable, surjective morphism from a scheme (no separation hypotheses), and let $\mathsf{D}(X)$ (resp. $\mathsf{D}_{\textrm{qc}}(X)$) denote the unbounded derived category of the abelian category of $\mathcal{O}_X$-modules on the lisse-'etale topos of $X$ (resp. the full subcategory of $\mathsf{D}(X)$ consisting of objects whose cohomology sheaves are quasi-coherent $\mathcal{O}_X$-modules).
For a representable morphism of algebraic stacks $f : X\to Y,$ there exists a functor $$\mathbf{L}(f_{\textrm{qc}})^* : \mathsf{D}_{\textrm{qc}}(Y)\to\mathsf{D}_{\textrm{qc}}(X)$$ such that $\mathscr{H}^0(\mathbf{L}f_{\textrm{qc}}^*\mathcal{F}[0])\cong f^*\mathcal{F},$ for any $\mathcal{F}\in\mathsf{QCoh}(Y)$. Moreover, $\mathbf{L}f_{\textrm{qc}}^*$ admits a right adjoint $$\mathbf{R}(f_{\textrm{qc}})_* : \mathsf{D}_{\textrm{qc}}(X)\to\mathsf{D}_{\textrm{qc}}(Y),$$ which does not in general agree with the ordinary derived pushforward $\mathbf{R}f_*.$ However, there is a comparison morphism $$\mathbf{R}(f_{\textrm{qc}})_*\mathcal{F}\to\mathbf{R}f_*\mathcal{F}$$ for any $\mathcal{F}\in\mathsf{D}_{\textrm{qc}}(X).$ (See section 1 of "Perfect Complexes on Algebraic Stacks" by Hall and Rydh for details.)
Let $f : X\to\mathcal{Y}$ be a flat morphism from an algebraic space $X$ to an algebraic stack $\mathcal{Y}$ over some base scheme $S$ and $\Delta : X\to X\times_{\mathcal{Y}} X$ be the relative diagonal of $f.$ Suppose also that $\mathcal{F}$ is a complex of $\mathcal{O}_X$-modules with quasi-coherent cohomology, and that $\mathbf{L}\Delta^*\mathbf{R}\Delta_*\mathcal{F}\in\mathsf{D}_{\textrm{qc}}(X).$
Does this guarantee that the natural comparison map $$\mathbf{L}\Delta^*\mathbf{R}(\Delta_{\textrm{qc}})_*\mathcal{F}\to\mathbf{L}\Delta^*\mathbf{R}\Delta_*\mathcal{F}$$ is an isomorphism? If it does not guarantee this in general, are there conditions on $\mathcal{F}$ which would make this true? I would be happy to assume that $\mathcal{F}$ is a genuine quasi-coherent sheaf on $X,$ and possibly more as well.
I'm interested in the question above, and potentially generalizations of it, but I would also be interested in an answer in the case when $X$ is a scheme. I know that this will be true when $\Delta$ is qcqs, but I want to avoid restricting my attention to this situation if possible.
Edit with further thoughts: As discussed in the comments, $\Delta$ is separated, but not necessarily quasi-compact. I haven't seen much in the literature dealing with the quasi-coherent pushforward for a separated but not quasi-compact morphism, so I'm not sure to what extent this helps.
One thing which could possibly be valuable is the construction of a natural transformation $Q_{X}\mathbf{L}\Delta^*\to \mathbf{L}\Delta^* Q_{X\times_{\mathcal{Y}} X},$ where $Q_S$ denotes the derived coherator functor $\mathsf{D}(S)\to\mathsf{D}_{\textrm{qc}}(S).$ This would construct a morphism $$\mathbf{L}\Delta^*\mathbf{R}\Delta_*\mathcal{F} = Q_{X}\mathbf{L}\Delta^*\mathbf{R}\Delta_*\mathcal{F}\to \mathbf{L}\Delta^*Q_{X\times_{\mathcal{Y}} X}\mathbf{R}\Delta_*\mathcal{F}=\mathbf{L}\Delta^*\mathbf{R}(\Delta_{\textrm{qc}})_*\mathcal{F},$$ which would hopefully provide the desired inverse. Of course, it could be too much to hope for that such a transformation exists in general.
Of course, one could find an explicit $\mathcal{G}$ completing a distinguished triangle $[\mathbf{R}(\Delta_{\textrm{qc}})_*\mathcal{F}\to\mathbf{R}\Delta_*\mathcal{F}\to\mathcal{G}\to]$ and then analyze (the cohomology of) $\mathbf{L}\Delta^*\mathcal{G}.$ I was trying to avoid an argument as explicit as this, but it could be the most fruitful approach. Does this strategy become any more reasonable if $\mathcal{F} = \mathcal{O}_X$?