instanced-mesh | The three | Graphics library

What is the high level goal when defining dependencies?

You have to define which dependencies you are using only when developing (devDependencies) and the ones that are needed when someone installs your package and are going to be installed automatic (dependencies), and dependencies you need to be available, but you want the user to install (which, honestly, does not makes sense) peerDependencies.

The difference here is that i don't define the class at runtime, and thus calling import MyModule requires react to be available in MyModule.js?

It would require React to be available where the file is being imported, i.e: A imports myModule, but A has to have react imported. Putting as peer dependencies is the best way here indeed.

For example using the externals thing with webpack vs having an actual import React from 'react'?

Using externals in webpack just tells webpack to not bundle react and says that react will have been imported before the import of this component.

If i set up my repo to work with the latest and the greatest of JS (or not even JS?), how and what should i publish?

Usually the index.js file that contains the library minified/bundled. Publish that with npm, you'll need to setup main field on package.json

import Foo from 'foo' //<-- where does 'foo' point and what is 'foo'?

foo points to the name of the package that you created, i.e: the name this package was publish under. When you go to npmjs.org and search for foo, that is going to be the package. foo is in your node_modules.