Linux kernel flushes all disk caches before going down. All the
halt/poweroff/reboot call sync before proceeding. You can even see a
message about it flashing extremely fast right before the
reboot/whatever initiates. Only thing that you can add is forcing
remount as read-only. That happens with Ubuntu as well. These measures
already do pretty much everything that is possible, and at least I can't
see anything else that would be doable.

I would instead of that focus on fixing the misbehaving applications.
(daemontools?)

-- 
Inconsistent filesystem on boot, possibly because of failed unmount on shutdown
https://bugs.launchpad.net/bugs/97645
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