Setting default user preferences

Hi, could someone please assist me in the best way to capture and essentially redeploy user preferences? 

I had three imagerunner 9050 scanners that accepted a registry change that would load the desired user preferences set in Capture Perfect 3.0 but after installed an imagerunner 1100 scanner, there no longer seems to be a way to capture user preferences and then redeploy them to any and all end users on the client.

Is there a reason why these preferences are stored in the C:\users\username\appdata\roaming location as a .dat file instead of being set in the registry under LOCAL_MACHINE? 

Thanks in advance