I had to do a lot of work on GJK convex hull distance back in the late 1990s. It's a optimization problem with special cases.
Closest points are vertex vs vertex, vertex vs edge, vertex vs face, edge vs edge, edge vs face, and face vs face. The last three can have non-unique solutions. Finding the closest vertices is easy but not sufficient. When you use this in a physics engine, objects settle into contact, usually into the non-unique solution space. Consider a cube on a cube. Or a small cube sitting on a big cube. That will settle into face vs face, with no unique closest points.
A second problem is what to do about flat polygon surfaces. If you tesselate, a rectangular face becomes two coplanar triangles. This can make GJK loop. If you don't tesselate, no polygon in floating point is truly flat. This can make GJK loop. Polyhedra with a minimum break angle between faces, something most convex hullers can generate, are needed.
Running unit tests of random complex polyhedra will not often hit the hard cases. A physics engine will. The late Prof. Steven Cameron at Oxford figured out solutions to this in the 1990s.[1] I'd discovered that his approach would occasionally loop. A safe termination condition on this is tough. He eventually came up with one. I had a brute force approach that detected a loop.
There's been some recent work on approximate convex decomposition, where some overlap is allowed between the convex hulls whose union represents the original solid. True convex decomposition tends to generate annoying geometry around smaller concave features, like doors and windows. Approximate convex decomposition produces cleaner geometry.[2] But you have to start with clean watertight geometry (a "simplex") or this algorithm runs into trouble.