Hey there, Bkeegan. Welcome. I see you haven't had the best introduction to this odd little place. Sorry about that.
OnTopic, though: The only reason I would "scorn" you is if you somehow forced me to use your method of AA, but you aren't and I'm therefore not personally affected by your decision. Ya know. We're all free to do whatever we want.
What program(s) are you using?
My biggest concern is that no machine automation can accurately AA your work for you, even if you define all edges manually by clicking point to point, tracing each sprite, etc. Your machine is still choosing what colors should go where. So you're robbing the finished product of being completely hand-crafted, and I'm sure the pragmatic AA pixel placement reflects this. AA'ing is an art in and of itself.
Secondly, yes, it's not precise. Your handing your palette over to your computer and saying, 'ok, have at it, make me some new colors!' When your computer doesn't know what's in the image (obviously). Hence, now you've got new shades in your finished product that are used only for AA. Not anywhere else. Logically, you would want to utilize these new AA auto-created shades elsewhere in your image - you can make smoother gradation between large areas of color, enhance depth, etc. The more you get into this type of hybrid technique, the more you step away from pixel art, and it's inherent benefits. Eventually, why not just go full-color and forget pixel art altogether?
And AA'ing your stuff isn't mucking up your work, it refines it. You could just as well manually AA on another layer, without the auto line transparency method. Using 100% layer opacity. This way you're protecting your palette. Surely, with this method of yours you have to do some manual clean-up anyway.
For the sake of the discussion, here's what I think you should do, and this will get you more feedback, for sure: post one your originals, with no AA, and then post the aftermath of your line tool technique being used to AA it. Having a visual to go along with this thread will help. I'm curious to see what you're pulling off, too.