Debian postinst script should not overwrite /etc/systemd/system/gitlab-runner.service
Debian ./postinst script calls /usr/share/gitlab-runner/post-install, which forcibly removes the runner service, and creates it anew. systemd unit in question lives in /etc/systemd/system/gitlab-runner.service, and as such all user-made changes there are lost.
Note that /etc is not /lib nor /usr/lib: it's expected that user might do any changes there, and all changes to /etc files that happen during package installation should go through conffiles mechanism, giving the user a prompt to resolve conflicts.
This is not even a Debian-specific convention. All Linux distros I know do the same with /etc/ (e.g. etc-update in Gentoo).