If you run through those steps, you'll notice you get an error on bundle. Additionally, if you look at the package in jspm_packages, you'll see it changed the import path from import * from '@joe-sh/jspm-empty-other-dependency' to import * from '@empty', which leads to the access error when trying to load index.js in that import path.
Kind of a hard issue to succinctly describe, so I've set up a repository where you can easily reproduce this issue https://github.com/josephschmitt/jspm-empty-demo
If you run through those steps, you'll notice you get an error on bundle. Additionally, if you look at the package in
jspm_packages, you'll see it changed the import path fromimport * from '@joe-sh/jspm-empty-other-dependency'toimport * from '@empty', which leads to the access error when trying to loadindex.jsin that import path.