All very good points, Bevo. To hit the stealth issue, first.
Comparisons to the B-2 are not very appropriate as that aircraft has coatings which have to cover a much broader frequency range than either the F-22 or F-35. The comparison to the F-22 is more appropriate and surly LM has had some time to get it much better this time.
You are spot on in the sense that the F-35 stealth is targeted in a narrower waveband, specific to pre-defined threats - although there have been questions about the currency of the assumptions at the time. The threats have moved on (L band sensors in the PAK FA leading edges for example), but it would not do the programme any good to try to change the specs now or to keep changing them. It is one of the difficulties with a programme that runs so long and suffers so many delays - before the acolytes get all upset, this is nothing new to the JSF programme, it's happened many times before.
I disagree, though that we can discount penetration or ballistic damage on a warplane. It HAS to be a consideration and cannot be swept away by statements to the effect that we've tested it to 600 hours of flight time (non-combat) and put a few scratches on the surface - against 8,000 hours without being retunrned to depot or manufacturer.
Even LM's engineers cannot design into the airframe the fact that it won't be hit by anything.
You statement about measuring total RCS post-repair in the field is exactly right.