But if you have a child company, wouldn't you expect to associate the parent company with a feminine gender before a masculine gender? That's what I am getting at. An organization has that "motherland" feel in some way.
Not really, no. Motherland is a very specific term that's been ingrained into English most likely because of the close personal relationship between people and their native countries, which would have been Britannia for many English speakers when the language was developing. There isn't really that same deep and universal connection when talking about organizations, so a similar term probably wouldn't develop anytime soon.
Sure, but what about ships? If you've read any sci-fi, the term "mothership" should spring to your mind. Or "motherboard" in hardware.
The concept of "some larger entity that spawns smaller entities" seems to generally lend itself to the mother/daughter terminology if you want to be poetic about it.
That said, whatever happened to artistic liberties?