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Bit late with my answer, but anyway:
StereoCalibrate calculates the transforms necessary to create horizontally or vertically aligned images. If your horizontal setup has a (slight) vertical misalignment, you get rectified images which do not completely overlap vertically: from one image a bit from the top is cut of, from the other a bit from the bottom.
As long as you have enough overlap for your application, the resulting stereo reconstruction should work fine, only with a reduced working volume.
I am actually working with a ZED camera right now, which has a vertical difference of about 10 pixels of 720, and it works OK when calibrated.
