Let $\mathcal C_0$ be a small additive category with countable coproducts, and let $\mathcal C$ be the category of additive functors $\mathcal C^{op}_0 \to \mathsf{Ab}$ preserving countable products. Then by Lemma 1.3 and Prop 2.5 here, $\mathcal C$ is a cocomplete abelian category which is easily seen to be locally $\aleph_1$-presentable. Moreover, cokernels are computed "levelwise", so that the representables are a generating set of projective objects; in particular, $\mathcal C$ has enough projectives. But $\mathcal C$ is pretty far from being an additive presheaf category.
Along with მამუკა ჯიბლაძე's example in the comments of sheaves on a complete boolean algebra, this makes it pretty clear that there are plenty of locally presentable abelian categories with enough projectives which are not additive presheaf categories. I'm still not sure about categories of quasicoherent sheaves, though.