Are you implying that getting init script customisations overwritten by package managers isn't a problem with non-systemd init managers?
I have lost track how often that happened with sysvinit, because the "logic" how to treat customisations was usually handled by the package manager and they messed it up regularly.
systemd has a standard way to handle customisations. As long as you put everything you do in /etc/systemd/system, everything is fine. It's simple and works across distributions.