1) The ICP alignment tool will indeed try to minimize the distances between the two clouds (and you'll get therefore distances centered about 0)... apart if you set the 'overlap' parameter correctly. If you set it to 10% or 20%, then only the closest points will be used for registration.
Of course, if you rely only on the point-pair registration tool, then you'll avoid this effect completely. This tool is much more reliable when dealing with heavily modified objects.
2) Isn't the registration error already quite high? (relatively to the scales, etc.). Can you try without it?
And don't hesitate to send me your dataset (cloudcompare[at]danielgm.net), it will be easier for me to help you.
Daniel, CloudCompare admin