Indeed. There are separate airlines called Virgin Atlantic, Virgin America, and Virgin Australia, but obviously the can't all be abbreviated officially to VA. So that's why Virgin America is VX, not VA.

And it's Virgin America which is going to merging with Alaska.

However: It's not been announced yet how Virgin America points might translate into Alaska miles. So it's a bit early IMHO to assume that a Virgin America card is a good value for what will eventually become Alaska miles.