Not quite sure how you know he took a copy of your passport if he took it out of sight.

In reality, an airline may tell a security contractor like ICTS to scan every passenger passport and visa or ICTS may mandate this. In reality, ICTS or, in cases where an airline provides the scanning equipment, only one scanner is likely to be provided. I used to buy one of these scanners from Air France Industries called ID Shield. It cost about EUR25,000 and you had to pay a subscription for software updates. Hence at this price you can't feasibly give each agent a scanner. Also it isn't always practical as check in areas can be small and congested.

in reality when profiling and verifying travel documents a Supervisor may decide just to scan the passports and visas of passengers whose profile has a suspicious characteristic. If you have an A380 or other large wide body with 400 plus passengers it isn't realistic to be able to scan all passenger passports during a check in window of 2 or 3 hours. A supervisor needs to get the agents to concentrate on those passengers who present one or more suspicious characteristics.

It is conceivable you may have had one or more suspicious characteristics for that route/airline.

If airlines and profiling companies did scan every passport unfortunately that would reduce airport capacity and increase costs.