Peace, Engines...
We seem to be mostly in factual agreement. The interesting thing is that discussing "penalties" or "scar weight" in the A/B/C context depends on which version is considered as the baseline - but thinking about it some more, this may be misleading, since none of the versions is the baseline.
The key to understanding the aerodynamic, structural and propulsion elements of the F-35 design is that no aircraft in history, that I can think of, has had such diverse and competing requirements imposed on it, along with a battery of non-negotiable constraints.
t was much more than what the late George Muellner described as "three versions differing only in how they took off and landed". CV requirements meant (eventually) quad tails and either a large wing, or the ability to accommodate two wing sizes. STOVL mandated a single large engine, located close to the CG, along with minimal OEW. Compatibility with different ships imposed limits on span and length. LO demanded large internal volume, translating into a rather broad body and an unusual relationship of net to gross wing area, and was unforgiving regarding changes to the mold line - all versions had to have the same wing sweep.
It would all have been hard enough, even without the USAF's willingness to die on the barricades to protect sustained 9g. For what it's worth, I don't think any of the designs submitted in 1996 would have done any better than the F-35. The engineers did their best, but there was no elegant solution to the problem enshrined in the JORD.