We want the UI elements in the settings dialog to follow the OOUI style guide. Note this is not only about the checkboxes. The buttons at the top don't fully follow the OOUI style guide as well.
This was originally meant to be part of T265709: Merge Page Preview and Reference Preview preferences, but split off into this separate task because of technical difficulties. The extension is build to be extremely independent. It appears it can't make use of actual OOUI elements because of this.
Note this is not a Regression. The two Save/Done buttons always looked like this. The two Enable/Disable radio buttons always used the browser's default styling.