Totally makes sense. The speakers, or should I say, many speakers, have projection patterns other than omni and especially the horns and tweeters in the boxes. If they are throwing a rectangular pattern of sound, as some are designed to do, then yes, simply flipping them 90 degrees will either give a very narrow sweet spot where they are heard or a wider sweet spot depending on their orientation.
If that pattern is also projected at an angle from the source, flipping them 180 degrees will affect them as well in how the sound is reaching the sweet spot and the ears of the listener.
This technology is used in sound reinforcement in churches and other venues to provide intelligibility to the sound by focusing the sound only where it's wanted and keeping it out of where it's not.
Good reading and good info. Many times folks simply set the speakers a certain way, as you said, because that's how they have seen it done or they think it looks cool. Experiment and see what actually works better and sounds better in your individual room. Don't worry about the looks, worry about the sound.