I added openntpd to my "root" tree. However, this caused it to fail and give up before my network was up. The solution seems simple: I'll just move the service to a tree that starts after my network is launched.

So I 66-disable openntpd in "root" tree, after stopping the service. Then I reboot. In my experience, a disabled service can linger in the 66-intree overview, but after a reboot the disabled service disappears. Most of the time. Not now, apparently.

I've been scratching my head about how to remove the service from the "root" tree. The documentation doesn't give me a clear answer. How do I reliably remove a service from a specific tree?
I know it must be in the documentation somehow, but from my experience using the -F and -S option saves me time, so if I want to stop and disable a service "on the fly" I use for ex: # 66-disable -t root -FS openntpd .
It also works with 66-enable if you want to enable&start a service.

From experience, to make a service disappear from being displayed in output of 66-intree,without reboot, you gotta use 66-update and make sure to use -d for dry run if you think there will be risk of fail...which is maybe always?
@ eric for some reason using the -F option, such as in the example you used, results the following output for me:
66-disable -t root -F ntpclient        
66-disable: fatal: ntpclient is marked initialized -- -F is not allowed
Expected behavior?
yes, this is an expected behavior. The -F remove all files about the service. This means e.g. the /var/log/66/<service> directory and other. So, if your service is marked initialized the 66-disable refuse to remove all the files. You can remove e.g. the log directory from a service that can potentially be started.
So first stop it AND unsupervise it like this 
# 66-stop -u <service>
Now you service will be not marked as initialized and so the disable command should works

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