I'm not sure the F-16 analogy holds true. There are still F-16s in service that were built in the 1970's that have gone through a midlife update with capability enhancements that exceed the original F-16C.
Indeed. So the F-16C became the definitive version of the F-16, whether as a new build or as an upgrade. It looks to me that F-35 is using concurrent engineering to try to avoid/bypass that early low capability version (whether its called "A" or "Tranche 1") and go directly (sort of) to the later higher capability/definitive version. Again, "trying" is the operative word. It's still unclear if they will succeed. But if they do it would appear that the early investment (in the from of cost over runs) will have been well worth it.