Hi Fraya,
My master program's transcripts was the final one, issued by UofT with all detailed information on semester, courses, grades (I completed all required courses in Jul, 2015 waiting for convocation in Nov, the transcripts was issued on 8 Sept,2015). Like you, I understood that final transcripts should provide sufficient information for CIC to process the PGWP but still they asked for School Confirmation letter (UofT issued the letter on 8th Oct, 2015 few weeks after I submitted the online application).