Maybe it is simply used for timing purposes from entering security to arriving at the scanner to give HAL advance warning when the time taken is starting to increase? To be able to better predict pax flows through security and deploy more resources accordingly? Gosh, how incredibly sinister is that, am petrified
I think most people who are anti the 2nd scan haven't got any worries about data protection issues. The biggest objection is the 2nd scan is meant to be used to see how long the average person waits in line. However, they often get you to scan it when there are still people in front of you waiting to use the trays and countless others queuing to go through the body scanner/detector - thus fudging the wait times.
Now if they had the 2nd boarding pass scanner as soon as you went through the body scanner, think that would give the most accurate timing.
As for made up rules - the lady in WH Smith T5 who told me I couldn't buy a pack of chewing gum without scanning my boarding pass.