Family Trees (& software) support adoption. The "genetic only" horse bolted long ago. Why support adoption for different sex couples but not same sex couples?

Sure, but I wasn't speaking for family trees in the social sense of the word. Of course these should include same sex adoption.

There are definitely uses for a genetic only tree, eg for medicine.

Depends on what exactly it is you want to map. From a purely genetic perspective you're right, but being a parent is certainly more than just contributing sperm/eggs. And besides - it's very hard to know if someone is indeed the biological father of a child, without resorting to dna testing. Who's the mother tends to be a bit more accurate, although that's also something that could be faked.

A complete graph (by some definition of "complete") documents the knowledge of who both parents are, and there are many situations where you cannot get such knowledge for practical or legal reasons.