I always associated these with key logging prevention. What drives me nuts however, is websites/apps that allow me to type my password but not paste it. Like they want to force that a keylogger can grab it?
Another favorite of mine are password conposition rules, which do nothing but reduce security and are everywhere :(
When I was a kid, a teacher told me learning was supposed to be hard and unpleasant, and I believed her for a long time. Only when I started enjoying myself in spite of that did I see it was wrong, and I started doing well in school, and (more importantly) pursuing my own interests.
There's a similar thing with security - people assume good security must be painful, so making it painful becomes a goal. Sometimes this is sincere, sometimes (TSA) intentional theater. But either way, the result is intentional hostility to the people who use the system.
I'd bet money they have a one-sentence answer for why it does each of those things ("order is scrambled to prevent shoulder-surfing"), but have done zero testing to determine whether those theories are correct.