Jetty 9.4 (I'm using 9.4.5, but it looks to me as though the source is still the same in the current 9.4.x and 10.x branches).
In the code for --add-to-start, the logic for (possibly uncommenting and) setting properties in the new .ini file intentionally only does its thing if the origin of the property setting was the command line (either directly or via --command). I understand that.
In the code for --update-ini, the logic for (possibly uncommenting and) setting properties in existing .ini files seems to do its thing for all property settings, regardless of their origin.
Offhand that seems to me like a bug, but am I perhaps just misunderstanding the intent of --update-ini?