In the universe that I came from as a Gem, on my Gem Homeworld, gender was a foreign concept that only applied to organic lifeforms. Gender, insofar as a Gems and Homeworld are concerned, only applied to biology.
I would say that in terms of social roles, Gem placement is the concept that comes closest in gem society to gender in human society, because it was identified with expectation of social role and personality type.
There’s no particular ‘reason’ that Gems take on forms that compare physically with human females. That’s just the way our bodily self images looked, even without contact with humans. I suppose I would say that Gems just have more qualities typically associated with human femininity rather than human masculinity. That isn’t to say that none of us had traits considered masculine!