From what I understand, the challenge is not so much the mechanics of the actual plunge, but rather how to position the machine, particularly on board A, such that the joint lines up as flush as possible. Since the plunge on B will be with the fence set at an angle, but the plunge on A will be without the fence engaged, you are worried about misalignment of the joint.
You could do some test cuts on some scrap boards to approximate the offset you'll need, knowing that the distance from the bottom of the machine to the center of the mortise is 10mm, and thus can set an appropriate guide/edge against which the machine will rest when doing the plunge on A. I like the idea of keeping the A board a bit long, and then trimming away the excess once you've done the mortises.