You could also mention Bad Horsie to give an example of Vai using low tuning . . .
It's very simple how he does it, he has certain guitars set up for those tunings.
He has more guitars than he can count (I read somewhere that he was given a Jem 333 by Ibanez to approve for manufacture and doesn't know where he put it), and he travels with a small army of guitars.
You can set up a FR properly with any tuning you want, it's just a pain in the tucas to CHANGE tunings OFTEN on ONE guitar. If you have 10 guitars you can have them all tuned differently, and each one can be set up properly (trem angle, action, neck bow) for that tuning.
With one guitar that has a floating trem, you would have to put up with the trem angle and the action changing (also a fairly long tuning process to boot) every time you want to change tunings, unless you block the trem. Either put up with that, or do a complete setup on the trem EVERY time . . . again, pain in the tucas.
There are devices that you can install that will lock the trem in place with the flick of a lever, or whatever (I've never actually played with one) and you can retune with the bridge locked with one of these.
You still have to worry about the string at the locking nut, and you can't use the bar while the tuning is changed (well, you can, but you have to unlock it, use the bar and lock it agian else your tuning will be all over the place when you let go of the bar), but again you see the drawbacks to this as well.
Plain and simple, if you want to chage tunings often, block or fixed, simply one of the "problems" you have to live with when you have a floating trem.
If you're not using odd tunings, just tuning down (like to play to a recording where the guitars are tuned down) you can use a pitch shifter, either one for the guitar to tune it down to the recording, or on the recording itself, to tune it up to your guitar . . . but some pitch shifters sound like crap, so get a good one if you go this road. ;-)