Currently we output by using the @@global-helpers.prepareGlobal method for reading the global as defined in https://github.com/systemjs/systemjs/blob/master/src/format-helpers.js#L284.
This method does global detection as used by SystemJS based on detecting the diff of the global object and making the new globals the resultant module value if there is only one, or an object with the global names as exports if there are multiple, with this behaviour being overridden by the exports metadata.
Ideally this transformer can gain the ability to do this detection as much as possible statically, and while never completely perfect we should be able to get a 99% accuracy for this to get equal behaviour.