The way I did this last year (through BCIT and Univ of Toronto, and with University of Pune), is to have the university of Pune mail my transcripts directly to these agencies. For this Univ of Pune needed an application filled, the required fees (through challan and all that cr*p, nothing online ), and my marksheets submitted in person. So I had to send my parents to do this. The university took 2.5 months to send the transcripts and I had to send everything required by Univ of Toronto, who took another month or so for evaluation. Not a smooth ride but got it done in the end.
I think all the evaluating agency cares is that your university should send a sealed transcript directly to them and that the names should match. So the transcript sent by the university + whatever else you are required to mail to them directly constitutes the complete package before they evaluate it. In my case last year BCIT and UoT matched my name on transcript and my name on application and did the evaluation.