My end goal is to have an animated skeleton and a variety of limbs that I can attach to it and have them skinned, which means I need the limbs to stitch together at joints. But to start simply I have 2 cubes, each missing a face and these cubes are side by side with their empty faces facing towards each other.
If I use Mesh.CombineMeshes will the 2 cubes attach at the open vertices? Essentially stitching themselves together?
No, they will not. They will simply be turned into a single mesh. It’ll be up to you to stitch them together.
There is some research on the subject, though they can be very technical (http://www.cs.cmu.edu/~mmv/papers/12irosw-BrandaoCosteiraVeloso.pdf).
However, keep in mind that all stitching means in terms of meshes is having two vertices in the same location in space. If your two cubes are exactly touching where you want them to be stitched, they will, for all intents and purposes, be stitched. If you go a step further and make sure that where they touch all the normals are identical (which they should be with aligned cubes), then they will even appear smoothly stitched for lighting calculations.