You do create it Motion. It’s pretty simple, really. The wipe matte should be black and white:
– the white allows the first clip to show through;
– the black allows the next clip to show through.
So, for example, you could make a wipe matte that’s a rectangle of black on the left, white on the right, sliding across frame from left to right (that’s if your transition is moving from left to right). If you dropped it into the clip well, it would reveal footage on the right, moving across to the left, like a basic wipe that you get in FCP’s effects folders.
If I knew more detail on the type of Alpha transition you want to make, I could give more constructive advice, having recently figured out how to do this for myself. It’s pretty awesome.