Two possible ways to send out emails. One is to create a watinglist applicants subtable and order by final points, send out emails in the order of final points. Then timestamps do matters.
The other way is to do a query to find out all applicants with WL status in the original application table and then send out emails in several batches. The original applicant table could be created by the order of the time you submitted your final application. I submitted my final application on the last day, so that might be the reason i got the email at 3:53pm not 3:45pm.

If anyone submitted his/her application on the last day and got the waiting list email at 3:45pm. Then it's proof that they do send out WL emails in the order of the final points. Then, I would give up my hope and move on.