Well, I managed to solve it. If I left out the kill_command, a real FM would get the trait client_ruler. If I used the "give_trait cheat in the console, the trait would be granted to a FM, irrespective of whether or not the puppet was already spawned.
No movement of the newly spawned puppet would happen, no matter what.
In one case that was the difference between controling a settlement and losing it to rebellion. In that case I created the character in the generic script, and commented out the client ruler in the EBBS.
However, I also found out the side-effect only occurs when the characters name is a real first name. So when a client is named "Marcvs", one of my FMs may suffer death at the hands of the script, but when the name of the client rules is something like "MarcvsK", that is fine, and did not result in any unannounced deaths. But perhaps I was lucky in the sense that I had no real MarcvsK as a family member?
I simply swapped around some client rulers' names in the script.
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