I don’t think you need to do anything except take the new rust.conf changes, since you are already using the new version of makepkg.conf. I am not sure why you would get a pacnew for one and not the other.
Note that debugging is enabled in the “stock” version of /etc/makepkg.conf (which you are using). Unless you specifically want that, you may wish to disable it. *-debug package conflict on system update - #10 by dalto