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.
I just learned that PROTON_ENABLE_NVAPI=1 to enable DLSS got changed to PROTON_FORCE_NVAPI=1 in Proton 9.0 (including Proton Experimental). Just in case this helps someone in the future.
On another note: Feel free to let me know if you've got a good way to keep up with necessary/useful launch options. I've simply been having a look at what people use on ProtonDB. But I've come to the conclusion that a lot of the posts there use outdated or simply false launch options.