Jay,

IMHO, there is no wrong way to tye flies. Some ways are considered and widely accepted as being better then others. Regardless, if you're more comfortable with one method, use it. However, I have looked through about 12 instructional fly tying books by renown tiers and the one you cited is the only one in which the hook is positioned in the vise like that. Again, if you're comfortable and it works for you, have at it.
Tight wraps.

Allan