For reference, this is Chapter III Proposition 8.5 in Hartshorne. The claim is this
Let $X$ be a noetherian scheme and let $f: X \rightarrow Y$ be a morphism of $X$ to an affine scheme $Y = \text{spec}A$. Then for any quasi-coherent sheaf $\mathcal{F}$ on $X$, we have $$ R^{i}f_{*}(\mathcal{F}) \simeq H^{i}(X, \mathcal{F})^{\sim}. $$ He proves this claim in the following steps.
Step 1: He begins by noting that $f_{*}\mathcal{F}$ is indeed quasicoherent on $Y$ since $X$ is noetherian. Taking global sections we find that both functors agree for $i=0$ when $\mathcal{F}$ is a quasi-coherent sheaf.
Step 2: He then notes that since $\sim$ is an exact functor from the category of $A$-module to the category of $\mathcal{O}_{Y}$-modules, both sides are cohomological $\delta$-functors from the category of quasicoherent sheaves on $X$ to the category of $\mathcal{O}_{Y}$-modules.
Step 3: He then notes that since $\mathcal{F}$ can be embedded into a flasque quasicoherent sheaf that both sides are effaceable for $i>0$.
Step 4: Bringing all these observations together he applies a result of Grothendieck that says that effaceable $\delta$-functors are universal and hence the two are unique.
My concern is that he seems to perform some unjustified sleight of hand in step 2. Suddenly we are only talking about $\delta$-functors from the category of quasicoherent sheaves on $X$. But this is not really the functor we are concerned with. These higher direct image functors, and indeed cohomology functors are defined out of the category of $\mathcal{O}_{X}$-modules. Indeed the category of just quasicoherent sheaves doesn't even have enough injectives so constructing cohomological functors out of it is meaningless. I don't see how this is enough to conclude the thing we actually set out to prove.
Is anyone able to put my mind at ease and show me how the original claim follows from these observations and effaceability?