“But not neccesarily in their final form. For example, one of the scrolls has Tehillim 145 (Ashrei), but it has a “nun” passuk (whereas, by the time of the Gemara, it was well established that there the “nun” passuk was omitted).”
That’s not a proof. In many scrolls this group tried amending the variations between Kri and Ksiv – to make them “grammatically correct,” similarly they would’ve tried amending what would seem to them “the missing Nun” of Ashrei – as they were a group which seemingly were Tzedukim and beleive in Torah Shebal Peh