Anonisstupid 
How do we know that ponies use genetics at all? Given the prevalence of magic in the world, couldn't it be possible that the soul itself is the basis of cellular function? Or that magic and genetics might both be at work? Maybe the expression of earth/pegasus/unicorn is a magical aspect while other aspects are genetic? Maybe all sapient life in Equestria is genetically similar enough to reproduce with one another, but the non-genetic/magical aspects are what give them different forms.