I have always turned bikes upside-down to work on them*. When I had dropped bars with delicate cables, I would put a small pile of books on the floor to support the bars and ensure that the brake cables weren't squashed.
With a flat-barred bike, that problem doesn't occur. With my Thorn, the Tubus low-rider rack allows me to remove the front wheel and keep the bike upright when the wheel is removed, so it is easier than otherwise would have been the case to remove the wheel with the bike the right way up. However, I have found that when I return the wheel to the drop-outs after the puncture repair, it is hard to seat the wheel in exactly the right place. It just drops right in when the bike is upside down and seats itself precisely.
*Actually, not so much with the tandem. I used to suspend that from the branches of our walnut tree as the tandem is far too big for me to turn it upside down easily on my own. It is much easier, however, to put it back together using the S & S couplings when it is upside down, and it's pretty well the only way to do it if I am reassembling the bike on my own.
I would be interested to learn how owners of solo machines with S & S couplings get on with reassembling their steeds after (e.g.) train travel.