Consider a surface $Ω$ with a boundary obtained by gluing together a finite number of equilateral triangles, or squares, along their boundaries, equipped with a flat unitary vector bundle. Let $Ω^δ$ be the discretization of this surface by a bi-periodic lattice with enough symmetries, scaled to have mesh size $δ$. We show that the logarithm of the product of non-zero eigenvalues of the discrete Laplacian acting on the sections of the bundle is asymptotic to \[ A|Ω^δ|+B|\partialΩ^δ|+C\logδ+D+o(1). \] Here $A$ and $B$ are lattice-dependent constants; $C$ is an explicit constant depending on the bundle, the angles at conical singularities and at corners of the boundary, and $D$ is a sum of lattice-dependent contributions from singularities and a universal term that can be interpreted as a zeta-regularization of the continuum Laplacian on $Ω$. We allow for Dirichlet or Neumann boundary conditions, or mixtures thereof. Our proof is based on an integral formula for the determinant in terms of theta function, and the functional Central limit theorem.