Quoting myself here:
the css settings box in the frame config modifies stuff in the frame (so anything on the website you're displaying), while the style: entry in the embed modifies the style of the frame itself (ie the box that contains the website you're displaying)
i dont think this is currently super well documented though. but essentially, anything you want to change on the website needs to go in the frame settings, and anything you want to change on the frame (ie the box in your note) needs to go in the style: thingy
Should be documented better in the README and potentially also just implemented more clearly somehow (like in the description of the style settings box?)