IIRC, someone on Sportbikes.net tried that YEARS ago and yes, the controls hit the tank. It's not a bad idea, in theory, but with the way the FZ6 tank "bulbs" out on the sides, you don't have a lot to work with.
If you've still got the fairing, then it's a whole other problem. I'm almost certain if you flipped the bars over they'd either hit the flat part of the fairing as it comes back to the tank, or it would hit the front part of the fairing next to the speedo.
You could try it, but it would probably be a waste of time. FYI, I've got the FZ1 bar and it's LIGHT YEARS better on my wrists than the FZ6 stock bar. But like everything, it's all personal. What works for me may not work for others. Then again, I'm thinking about trying clip ons soon...and that wouldn't sit well with someone looking to take pressure off their hands...lol.