for example, if squid needs some directories to exists before initial run after boot, it could set this in /etc/rc.d.conf/squid

squid_opnsense_bootup_run="/usr/local/opnsense/scripts/proxy/setup.sh"

which effectively results in setup.sh being started followed by the normal service squid start

disadvantage of this, both the service template and the rc system needed to be aware of the setup.
advantage, all services which don't need special preperation are configured as they would be on normal FreeBSD