This is highly dependent on distro, but for any use-cases where editing /etc/ is the recommendation, I have found that either:

(a) It's a development environment thing (e.g. httpd vhosts) & thus I see it as quite separate to "my dotfiles" (a personal machine env thing): I try my best to manage dev env stuff from project-specific repos wherever I can (i.e. a bash script to dispatch required local /etc/ changes in a repo "./scripts" dir or similar), or otherwise if it's a more significant set of configs, Ansible.

(b) It's a specific app that is recommending doing things the "Wrong Way™". There's often a workaround to get it to use $HOME or $XDG.

(c) It's OS package configs. I've found that things like repo & key installs are well suited to chezmoi run_ scripts. For anything more advanced or esoteric, I guess that may be an exception.