When you arrive at Swampy there will be a TE rep meeting you at the gate. They escort you to the express entry lane in Immigration. It is in a separate area from the main Immigration queues. When I arrived there was noone else there. I sat down while the TE rep and the Immigration Officer sorted out the visa and added it to my passport. I don't think it is very likely to be rejected at that point, it's not like you are at the mercy of the main Immigration queue as to which IO you get and if they are having a bad day.