It' a tough one to answer, since there are apparently many kinds of flyaways - caused by bad GPS, bad Gyro's, or faulty RC signals (or over-riding signals).
Manual mode will only really help in the case of bad/stuck gyro's I believe.
But since you can indeed initialize RTH by shutting off the Tx (generally), if you're really concerned about recovering from such a flyaway, enabling manual mode might not be a bad idea, just so long as you don't accidentally flip the S1 switch too far.
I think it's ok to try/practice manual mode with the Phantom, so long as you're in a wide open field and well above ground.
the key is putting the Phantom in a hover prior to do so, then enable Manual mode and try to maintain altitude (it might go UP or down really fast). and then very cautiously and subtly move the right stick and yaw controls and go from there.
I've only done it a few times, and it scares the hell out of me. (but I enabled manual mode on a separate switch on my Futaba).
of course, under non-flyaway situations, the key is flipping back to GPS the moment you feel uncomfortable!
under flyaway conditions, I'd say manual mode is great for bringing the craft down in a semi-controlled manner.