According to my own experience, this does not always work.
Example: The file /usr/share/X11/xorg.conf.d/10-nvidia-drm-outputclass.conf gets overwritten each time linux510-nvidia390xx gets updated - without a *.pacnew file being written 
Another example: In order to get Qoppa PDF Studio to recognize my scanner that is connected via the network, I had to modify /usr/lib/systemd/system/saned@.service. See Sane: Share scanners via Network? - #5 by DAC324 for details.
This file gets overwritten on each update as well