I am no expert on game developing (my expertise lies in desktop applications), but from what I have seen so far, it looks like they do use separate branches in source control, considering the build shown in their live-stream a while back was far more advanced that this alpha build we will be getting is (judging from what they said in the stream itself, and other things I have seen on the forums here).
As for why they didn’t have a branch all ready to go for the alpha release, if they had it ready, why would they delay releasing it? It wouldn’t make much sense to me to have a stable alpha build sitting around, waiting to be released when it is all ready to go. I assume they just misjudged how much time was left to get the alpha version to the point they wanted it for release.
Again, I am no expert, but that is my thought on it.