From what I can see, there is no border coming from the theme CSS, the border comes from the Browser user agent stylesheet.
The border is still set as border-style inset by the browser, but the two colors used to make the effect are very close grey (133 and 118), and so it looks like a uniform dark border instead on giving the emboss effect.
That change was maybe made by the browsers because the old emboss style looked old, and they may have decided to modernize it…
@weaver Can decide if he wants to enforce a different default style to override the new browser default (if that is what it is).
You can also impose your own style by adding the CSS to style the border, using the selector