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.
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.
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.