I had the same desktop layout as yours and was looking for the same solution. I think buttons are not gone but are hidden under the top desktop bar. I did not want to resize Opera window or move the top bar, so used it as it is, but can say it was not a big issue at all. If you set that second click on the program's icon in bottom launcher minimizes/maximizes a window you can do that from the launcher and for me, that was a much more convenient way. So the only thing that I would use top buttons was closing the program. I used a keyboard shortcut Ctrl+Q and must say you get used to it very quickly.
Opera for Linux
