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FYI I bought a set of the new Quick Jack extensions for my 5000TL. They fit great and will totally eliminate the alignment issue. However I don't remember reading that they would drop the lifting capacity but when they arrived they are labeled at 4000 lb capacity max. That was a major surprise to me, but since my models wet wait is (theoretically) about 500 lbs lower it should be OK. Still I felt very comfortable with over 1000 lb cushion!
The factory guy told me that the drop-in's were developed after customer's had noted more of a fitment problem for the C5/C6 with the new taller 24" rise 5000TL model than it was with the older 21" raise 5000SLX models. The drop-ins can be used with either the newer or older 5000/6000 models.
They also have a similar set of drop-ins for the higher lifting weight 6000/7000/8000 models too.