This is Japan, since the dawn of time everything manifests as an appealing member of the opposite sex. there.Doesn't really seem like there's a point in making the tree's spirit a woman unless there would be plans to do things together, like maybe romance. It could have been a disembodied voice, and that frankly it would have been more fitting given the spiritual nature the author seemed to be trying to portray.
That aside, it's a cute story.
I remember a manga where a guy fucked a sexy tree with hole ("todo hueco es trinchera") and was gaia xD, was fun their son/daugther, I dont remember the name
Saplings rise up