Some aren't reinforced and would shatter upon any sort of impact, giving another chance for injuries that wouldn't have been there before. The idea of child safety restraints are to eliminate and prevent injuries.... so the handle positions, in my eyes, would be another piece of the prevention part.
That's exactly it. The allowed positions are the ones that the manufacturer has tested it in and found acceptable. (In the case of Graco, yes, the engineers said that they would use it all the way up, based on what they saw; Combi also requires the handle up on some and highly recommends it on another infant carrier, in large part for this reason.) If the position is not allowed by the manufacturer, either it's been tested and found unacceptable, or not tested and to use it in that position is taking a gamble on whether or not it will harm the child.