That's a really good question.
I think I remember reading somewhere that Pristine versions of player-made scrolls would yield App4 spells and that this feature would be implemented in a future patch, maybe the big one headed this way in early January.
As it is right now, I can't tell the difference at all. I've made a Pristine version of a low level skill for my Bard and it seems not to be any more powerful, relatively speaking, than an equally low level spell for my Necromancer that was only Shaped quality.
Right now, I wouldn't bother trying to make Pristines >unless< it isn't all that much extra effort for you to not only make the finished product but also the interim ingrediants.