Maybe I'm missing something, but isn't the main 'hook' for this library that it looks native? Looks like it uses GTK+, so from a technical standpoint it would be as "native" as Qt.
That sentence you quote is immediately underneath the heading "Problems using virtualenv under Ubuntu" — it applies only to Ubuntu, where they do use GTK. But on Mac, they use Cocoa, as stated in several places in the docs.
Project author here; let me confirm that Toga only uses GTK+ under Ubuntu/Linux. On OS/X, it uses Cocoa. I've just clarified the text in that section of the website. Thanks for the heads up.