Hello,
I believe the difference is that files in /usr/local/directadmin/data/templates/ are updated as DA is, while the actual in-use configuration files on DA systems are not updated. However, note that some of the files in /usr/local/directadmin/data/templates/ are directly used by DA and do not exist anywhere else on your server.
If you want to prevent a file that is exclusive to /usr/local/directadmin/data/templates/ from being overwritten as DA is updated, you can move the file into /usr/local/directadmin/data/templates/custom/. When DA is using them, files in /usr/local/directadmin/data/templates/custom/ will take precedence over same-name files existing in /usr/local/directadmin/data/templates/.
Cheers, Phi1.