In theory by having the roll COG of the axles different could affect handling yes. Basically your axles will shift left and right a different amount when traveling up and down. Will it be enough to notice IDK but that's the rough idea of it. In my old 08 I had the rear raised but didn't have a flip on the front and it drove just fine for 3 years. I will say though that once I flipped the front it drove much better but I had a whole host of other issues when I re did the front of that Jeep so who knows.
I am contemplating flipping the front of mine as well and for now I didn't plan on raising the rear unless it felt funky. But if you have the bracket already and you can make it work I would use it, but if it doesn't work or you need to order a different one I wouldn't be all that worried about driving it with 1 raised and the other not
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