I too have been very frustrated with this, but it just occurred to me to try circumventing the issue with BetterTouchTool & it's working splendidly. If you don't want to pay for BTT, there is a free alternative called Jitouch which is pretty solid. I would highly recommend either/both of them for a wide range of immensely helpful uses as well as this specific issue.
In short, this is what the fix involves for either BTT or Jitouch:
(1) Make sure you have keyboard shortcuts tied to the Back and Forward functionalities in Opera settings.
(2) In BTT or Jitouch settings, map three-finger swipe gestures to their respective keyboard shortcuts. I would recommend configuring the gesture settings to be specific to the Opera app, so that it doesn't interfere with the native three-finger gesture functionality in other apps.
Not ideal, but as a workaround it's easy & effective enough to get by until Opera fixes the bug.