I am trying to learn this specific linux and how it works.

What are the upgrade policies as far as config files and directories not in the users /home?

For example, I have added/modified things in /etc/modeprobe.d, /etc/ld.so.conf.d/, fstab of course.

Will any of these things ever get overwritten while using the pacman system update command?

With pacman configuration files are not overwritten, on updates pacnew files are created (as an example).

See line 14 on the PKGBUILD:

At times a pacmerge is needed to merge updates with your existing settings.