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The derailleur can be adjusted just fine with the bike upside down.  Flipping the bike doesn't change the side to side alignment of how the chain is fed to the gear set.

However, one thing to watch out for is pinching your brake cables.  If the brake cables go straight up from the levers on the handlebar, then they will be squished against the ground when the bike is flipped.  I usually put a 2x4 under the handlebar to act as a spacer.

When out on the road and the derailleur seems to need a little adjustment, I just give it 1/8 turn in the appropriate direction and ride some more.  It shouldn't be far out of whack by the time you ride the bike anyway, so usually not more than two such adjustments (1/4 turn total) is necessary.