How to aggregate JS assets on Mean.io
It turns out it was aggregating assets well. As Mean.io docs say
All assets such as images, javascript libraries and css stylesheets should be within public/assets/{img|js|css}/ of the package file structure.
By default all javascript is automatically wrapped within an anonymous function unless given the option {global:true} to not enclose the javascript within a contained scope.
It's then when you are able to use the external JS functionality.