Since you are providing a way to pass options to Uglify directly (separate from SystemJS Builder defaults) these should be consistent with UglifyJS.minify(). minify() has no option beautify but has output^. This is passed in your code to ast.print_to_string(outputOptions) which is the same as what minify does internally$ except for this name discrepancy. See lines 106-113 in lib/output.js.

To be consistent with uglifyJS this must be changed.

^ output has an option beautify inside.
$ print_to_string() is a wrapper for function OutputStream() which is what minify invokes directly.