When the muffler is above the engine raw fuel can run back into the engine. My experience has been hard starting when the engine is rich or over primed. Sometimes enough fuel will run back into the engine to cause hydraulic lock. Some muffler designs are worse than others but it is preferred for raw fuel in the muffler to run out the tailpipe. I recently mounted an engine upright for cowl reasons and it is a pain in the posterior and will need to be remounted.

Ninety degree mounting also usually looks better.

Rotating the engine usually helps keep fuel off the wing.

Rotating the engine almost always helps to maintain the correct CL of tank to CL of carb relationship. The height of the carb relative to the tank is very important for proper engine operation. Get the carb height wrong and there will be no end of troubles.

Bill