The good news: My ECA was completed exactly on time (29th Sep)
And to answer my own question, it didn't matter to them that my name was slightly different on the transcript.
Though they did make a note about it in the report. I suppose I will have to write a letter or something to explain all this at a later stage.
As for the timeline:
1- Application creation and submission: 19-AUG
2- Documents (Transcript + Certificate) sent from University: 24-AUG
3- Documents delivered: 30-AUG
4- Documents received and accepted: 12-SEP
5- ECA completed: 29-SEP (so it took 17 days since they accepted the documents)
Overall, the process was fairly straight-forward and certainly within the time they mentioned (20 days).
I also never contacted them even once for anything.
Now the bad news: When I submitted my express entry profile it said I'm not eligible even though I'm quite certain that I am

That's a topic for a different thread though, good luck to everyone else still waiting.
EDIT: never mind, it was a stupid mistake on my part!