It might be that your distribution of choice has slightly different defaults in the files compared to regular Archlinux.
Either way you’ll want to have a look at either Meld (graphical) or something like pacdiff (terminal). With these you can easily see the differences between your old file and the new .pacnew.
The new default is not always better. One example: Whenever Archlinux creates a new /etc/makepkg.conf.pacnew I don’t simply overwrite the old file. The new default would comment out the line which defines how many CPU threads I want to use to build packages and reduce it to one thread (I assume).
You really don’t have to understand every line in every file. Most often it’s quite easy to determine whether you want the new changes or not. Just always have a quick look at what is different. You don’t want to replace old files mindlessly.
Paru has this funtionality build in. I don’t remember whether it is enabled by default though.