Again, it depends on the system and the limitations. You can most certainly remove the bottleneck through settings, but no it may not work for all MMOs. Some offer onscreen avatar options and locking it to a fixed number most certainly can alleviate the issue.
Options are there to be used, if you want a certain experience there are trade-offs, and I never said it was ideal. But claiming definites isn't entirely accurate either.
It, like any other game, depends on the settings used. If someone told me they had 60 FPS Solid EVERYWHERE in FFXIV using Maximum settings I'd call them a damn liar. If they said they had solid 60 FPS every where using Desktop (standard) I'd be more likely to believe them.
For starters FFXIV uses a character limit cap (ie only x-amount of people are ever shown on screen) which alleviates a lot of the CPU bottlenecking. The rest is alleviated through turning off other dynamic functions.
You'd be amazed how much of a penalty just using shadows carries. Toss in real time reflections and your PC is working overtime.
Powertune works from my understanding on on-demand power requirements. IE if you have excess power to offer, the card will use it. From my understanding is everyone just sets it to +20% and only negative when they are trying to underclock. I normally keep mine at 0%.
As for Windows Index, I don't think it tests multi-GPU settings. And since a single core on a HD 7990 is often clocked slower than a stock one, and a stock one (not Ghz edition) is on par with a GTX 670, it seems about right.