Outside the core of the plasma, the plasma current and pressure rapidly transition to zero in a scrape-off or edge region or plasma-vacuum interface. However, existing tools for fixed-boundary magnetohydrodynamic equilibria in 3D toroidal domains (stellarators) typically prescribe the computational boundary interior to this transition layer, and these equilibria are used for stage-1 optimization of the stellarator physics properties. We (1) argue that a more realistic and robust assumption is to define the computational boundary exterior to this transition layer, in a vacuum-like region, (2) show that, without this boundary change, existing coil optimization routines for stellarators should be changed to match free-boundary equilibrium requirements, and (3) derive an algorithm for a fixed-boundary 3D equilibrium solver compatible with a very general computational boundary. Moreover, stage-2 stellarator optimization (finding feasible coils for stellarator fusion devices) is a critical challenge for realizing this concept for future power plants. To rapidly speed up and automate the workflow of designing stellarator coils, we have designed an end-to-end “runner” for performing stellarator coil optimization. We also construct a novel in-the-loop optimization of Von Mises stresses in the coils, opening up important future capabilities for in-the-loop finite-element calculations.