All ChromiumOS firmware components and support tools are open source (minus vendor blobs on certain platforms). The 'crossystem' and 'futility' (which contains 'gbb_utility' which is called by the set_gbb_flags.sh script) tools are part of https://chromium.googlesource.com/chromiumos/platform/vboot_reference/+/mast... .
set_gbb_flash.sh ultimately calls flashrom to update flags in the ROM, which should hopefully "just work" under FreeBSD (assuming flashrom's FreeBSD support is as good as the README suggests). 'crossystem dev_boot_legacy=1' ultimately writes to CMOS on the C720 through /dev/nvram, which seems to exist on FreeBSD so if you're lucky it will also just work. (Note that if you were using an ARM Chromebook instead, it would need to write to the embedded controller and you'd be out of luck unless you wanted to port the (also open-source) drivers for that.)