From initial testing, this bug ("transparent button background results in a loss of the default button focus styles") doesn't seem to manifest itself anywhere in Bootstrap (since we don't just set transparent background anywhere on buttons, and when we do set explicit button styles in the more specific stylings, we already do create a custom :focus style anyway)
Incidentally, this forced definition of :focus is biting us in the rear because it essentially circumvents the browser logic that only applies focus outline based on the browser's heuristic (i.e. not applying the button outline when clicked with a mouse). this forces the focus style to always show even after a mouse click, which is causing is hassle that we then need to work around - see https://github.com/twbs/bootstrap/pull/32630