>the various ACME clients like acme.sh are run with elevated privileges
Its really not that difficult to not grant excessive privileges - at the very least for recurring ("cron") runs, once filesystem structure, cache invalidation triggers and web server configuration are in place. Its a shame this is still taught in the "just run as admin" style.
That capability should be added to acme.sh, etc so that it automatically runs with minimal privileges for the invoked task. But people seem to assume privilege management is the sole responsibility of the packager or caller, despite the tool itself being better placed to know precisely which privileges are needed for the particular task it's performing.
acme-client on OpenBSD does this, using privilege separated processes that each in turn use pledge and unveil. You wouldn't know without looking at the source code because it's entirely transparent.