I believe the rational was to encourage skaters to perform jumps that they can actually, technically do. A triple jump with over more than a 1/4 rotational deficit is not a triple jump and should not get the same base value as one that is fully rotated . A jump with a small UR ( skaters do have to start trying the more difficult jumps under pressure and this is when you should see small under rotations). This should be penalized by the GOE. A skater who obviously is performing jumps above their skill set ( and get down grades) should be encouraged ( by being told through a protocol) to work on these jumps.
That, to me, can justify why a jump is downgraded. It doesn't, however, justify downgrading a jump and at the same time giving the jump negative GOE.
Besides, skaters are sometimes downgraded for jumps that they can "technically do". There are several example of skaters who have certain types of jumps downgraded in one competition but not the previous or the next competition.
... a downgraded jump should not get full credit ( we see way too many cheats as it is, I would not want to encourage skaters to fill their programs with poor technique ), and should be penalized for the mistakes in the jump phases as well as for the obvious UR.
By mistakes in the jump phases, you're referring to your previously mentioned air phase as one of the other phases. You did not provide a source for that and I believe that you're mixing that up with a different set of rules. A jump may get negative GOE for the air phase, but that has nothing to do with whether a jump is downgraded or not. Jumps are downgraded for only two reasons:
* more than a 1/4 turn under-rotated
* or "a clear forward takeoff" (too pre-rotated) on the 5 types of back jumps.
http://www.usfigureskating.org/content/First-Aid-Single_2007-08-15.pdf (page 50)
Besides, "should not get full credit" is a far cry from getting less than half credit AND then negative GOE on top of that.
Let's use a practical example. Nakano got 7.30, 7.50, 7.50, and 2.24 points for her 3As in ISU events this season. The base value of a 3A is 7.50 points and the base value for a 2A is 3.50 points. Nakano's 3As were very similar in quality. Simply put, the high variabililty in the scores shows how poorly the under-rotation rules accurately reflect the quality of the performances. When poorly supported theory has been debunked by practical examples as it has this past season, I think that it's time to fix it rather than support it.