Not sure if I'm looking at the right CommonJS spec (the commonjs.org-site is a bit confusing), but in the current jQuery plugin template (jqueryPlugin.js, line 7) module.exports is used instead of the CommonJS standard exports.
You can compare this with commonjsStrict, line 23, which does check and use the exports-object – not module.exports.
I think jqueryPlugin.js should be changed to use the exports-object.
Note: Both files were checked at commit 95563fd (latest master as of 23rd Dec 2016)