This is an increasingly solved problem in the post-systemd world - /etc contains local configuration, system configuration is in /usr. We (CoreOS) support you doing mkfs on / in order to return to a default configuration built from the /usr config.
https://www.freebsd.org/cgi/man.cgi?query=beadm&sektion=&man...
NeXt->Apple also avoided anything like systemd via a configuration system that supported inheritance across search domains (User, Local, Network, System):
https://developer.apple.com/library/mac/documentation/Cocoa/...