Thanks for the return visit, duncanm! I agree that it's odd that Opera lacks better skinning functionality -- especially considering how customizable it is, otherwise.
Regarding WB versions, I'm actually not using the latest one. So the problem is not limited to that.
I have, at least, found a workaround:
If I make any settings change in Flags, and then restart Opera, the program avoids getting skinned by WB at all. That restores the missing components (Window control buttons, etc.). This accomplishes what the WB "ignore this app" command is supposed to but doesn't. Annoying, but it works. Of course, this means having to keep the browser open all day to minimize the annoyance; but I don't find that to be a problem. I mean, not on the scale of global warming or anything. Really, when you think about it, software is just a bunch of electrons getting herded by programming cowboys. (ecowboys?) It's amazing that it works as well as it does.