etc/beats/metricbeat.modules.d/system.yml seems like a great candidate for a .sample file
It would avoid this situation:
$ sudo pkg check -s
Checking all packages: 1%
beats7-7.10.1: checksum mismatch for /usr/local/etc/beats/metricbeat.modules.d/system.yml
Checking all packages: 100%
I imagine that local changes to that file are common. Upgrades shouldn't overwrite them.
I don't know about the other 572 .yml files in pkg-plist though...
Thanks for the feedback, this will be included in next update.