Actually if a skater loses enough speed that the (second or) third jump is underrotated, wobbles on and off the wrong edge, etc., then they probably will lose GOE.
Look at Jeremy Abbott's three-jump combination in the long program at Nationals this week:
http://www.usfigureskating.org/leade...6/results.html
He lost 1.5 in GOE on that element, so he probably would have been better off not doing the third jump, which was where the problem was.
Because it isn't easy to maintain speed through three jumps, when skaters do manage to keep a running edge on a third landing, it makes sense to reward them.
On the other hand, judges also want to see landings with really strong landings, good speed and control, which is most likely to happen with solo jumps. Hence the limit on the total number of combinations, which has been around a lot longer than the IJS.
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