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In case it helps anyone, the command I ended up using was:
sysupgrade -v /tmp/firmware.img
I put this inside a small wrapper script and used crontab to schedule it. The devices successfully updated in the middle of the night from RUTX_R_00.07.02.2 to RUTX_R_00.07.02.4.
The config was preserved, but a couple of scripts I had in /root were erased (which is expected I guess). I don't know if there is a safer place to store any scripts so they will be preserved during sysupgrades. But that's not a major issue.