It makes absolutely no "chemical" difference which is added to which. The old high school saying "do as you oughta, add acid to watah" admonishes you to do this ONLY because when you pour one liquid into another, if there is any splashing, the liquid that you are pouring the other into is the one that is going to do the splashing. I regularly do it the "wrong" way... ::
I USED to sometimes use other stains in conjunction with AF, basically because I either did not know what I was doing, or there was a big screw up...I have a gun that I stained and neutralized and later decided to rework (the fore end was too thick mostly, and I reshaped the wrist some, etc.) Well, once the stain is neutralized, that's it. Staining the stock again is nigh on impossible. I washed that stock, stained, washed, stained, stained, stained. I like to have never gotten the stain to "take" on the wood again, and when I did, it was not quite as even as I would have liked. I made the stock overall quite dark by using an aniline dye-colored "Danish oil" stuff in order to even it out. I don't really recommend this course of action, but this was an extreme circumstance.
None of the guns that are on my photo album are stained with anything other than AF and neutralized with lye.
http://photobucket.com/albums/v326/Fatdutchman/Flintlocks
I have recently taken to the idea of no stain at all. I've been seeing more and more old guns lately that have never been stained with anything and have been finished with plain brown varnish or even a red "violin" varnish, which I am quite fond of. I'm working on a Lehigh gun right now that will sport this unstained, red oil-varnish finish.