I'm not sure, but a flipped over bike might actually be resting on the shifter bodies themselves -- I don't want to set my bike on expensive plastic bits that are easily scratched -- or broken. Plus, a road bike flipped over isn't incredibly stable because the bars are narrow. IMO, it's easier to remove and install wheels when the bike is right side up.

And, it's a good idea to have the bike right-side-up when you tighten the skewer, to help ensure that the axle will be seated into the bottom of the dropouts.