Again, the fenders have nothing to do with the suspension, which is what an alignment is adjusting. An alignment is for getting the vehicles' suspension to properly work, efficiently and evenly.
If you purposely raise/lower one side to be different from the other(the suspension, not the fender), the handling will change in how it turns left versus right. You may not feel it, but ask someone in NASCAR why they play with corner "bolts" constantly, to improve the handling.
You could raise or lower a fender by a foot on either side, and the handling would not be affected. But when you go and purposely alter the suspension height on either side(from true level), the handling is negatively affected.
I know that I'm being picky, but for very good reason. Rarely does anyone notice a different fender height, so that's a vanity thing, don't harm vehicle handling to fix that. There are dozens or more people who will read that and not recognize the negative affect caused, unless someone like me points it out to them.
This thread is about fuel economy, if you go and **** the suspension too far away from level(to make the fenders pretty-level), mileage will be lost.
FYI, my 98 fenders were off by right at 3/4" from each other, it had very minor LF fender damage at one time. It would have been very stupid of me to level those instead of the suspension. Good luck,