In the years since this question was asked, some of the theory the OP wanted was developed. First, in Lurie's Higher Algebra, Definition 7.3.2.14 defines the absolute cotangent complex functor $L: C\to T_C$ associated to a presentable $\infty$-category $C$. The next section deals with relative cotangent complexes. This theory is generalized in Lurie's Spectral Algebraic Geometry, Definition 17.1.1.3 and Variant 17.1.1.4 (for the relative version).
Y. Harpaz, J. Nuiten, M. Prasma extended this theory from $\infty$-categories to model categories, in the following three papers:
- The abstract cotangent complex and Quillen cohomology of enriched categories, arXiv:1612.02608.
- Tangent categories of algebras over operads, arXiv:1612.02607.
- The tangent bundle of a model category, arXiv:1802.08031.
Furthermore, Porta and Sala's 2022 paper Two-dimensional categorified Hall algebras works out the connection between cotangent $\infty$-categories and coherent sheaves (see especially 2.3 and 3.2) and includes a discussion of cotangent bundles of quivers on page 10. There, they relate the cotangent stack of a quiver with cohomological Hall algebras, and recover the description in (2) of the OP. There they cite:
See also 2.3 of the Porta and Sala paper Simpson’s shapes of schemes and stacks, from 2020. My expertise is really more on the model category side, but hopefully these references help (and get this old question off the "unanswered queue").