Pros and cons.
The exhaust port area gets hot vs the intake side which actually is cooled, so the temps should be much more even with it orientated the normal way while riding.
Flipped it gets more fresh cool air into the motor though which means more power, and you can easily make a ram air effect for the carb if you wanted (and if you did 50+mph where it will actually do anything). I planned on testing a flipped cylinder setup with a 3d printed adapter and some ducting for true ram air to test gains at 50mph but never got around to it.