For what it's worth, I have found Alden's recrafters to be very generous in their application of pigment in the absence of instructions to the contrary. When I sent in an old-ish pair of shell captoes for resoling, they left a very well-worn light burgundy, and they returned the deep purplish color of brand new color 8's. Lesson learned - next time I will give very specific instructions.
Also, it seems to me that your longwings appear to have been on the darker/reddish side of whiskey to begin with. When I saw your "after" photo I was shocked at how dark the shoes are, but in comparison to your "before" photo they don't seem so different. For comparison here are my only pair of whiskeys, which almost appear a different color altogether from your "before" picture (of course different lighting could also be at play):
This is not to say you should be satisfied with the result. If you are at all unhappy I think you should send them back and ask for a new pair. Frankly I think your shoes were too dark to be called "whiskey" to begin with, and that already reflects a QC problem on Alden's end. However, they are an interesting shade and possibly more useful IRL than a lighter whiskey pair, so there is no shame in deciding to keep them if you like them for what they are.