The settings in the default user options in MessagesXx.php files (where xx is the wiki content language), have no effect. The value is overridden by the values in DefaultSettings.php. When removing an option from DefaultSettings, it uses the value again from MessagesXx.php
This bug is present for quite some time, since the defaultUserOptionOverrides are almost only used for quickbar (used by some legacy skins) by RTL languages, which is a small userbase so it didn't get noticed.
(Interesting side-note: in the case of quickbar for RTL languages, this bug is being "corrected" by another bug: CSS for RTL languages is flipped, so where "left" is the default option, it's flipped to "right", so your preferences will say you have left, while it's right, which it should be, but because of MessagesXx options and not because the CSS it's flipped)