Just thinking out loud. (Sorry for the political angle.) Pentagon is the party most dependent on Turkey to produce the F-35 components. But it's also the Pentagon that pushes the block on S-400. It looks strangely superficial and conflicting. You just don't push away the country that you depend on so much for a program. And S-400 is far from new. It can't be such a huge threat. If anything, Pentagon should be interested to see how it performs against its planes and work on countermeasures.
We know Erdogan is not a pushover and will likely react in some spectacularly explosive fashion. It's also very likely that Turkey leaving the program will delay the program even further and make it even more expensive which in turn will justify the Pentagon to pull the plug on the whole shebang. Can it be that some faction in the Pentagon are simply trying to get rid of the program this way?
Lockheed is a great innovator but their innovations are always so "ahead of its time" that they take decades (and a lot of money) to realize, and by the time they are flying, it's too late and nobody wants (or needs) the aircraft they produced, and the technology has stepped further forward making the aircraft irrelevant or even obsolete. I'm thinking about SR-71 - by the time it was ready to spy on the USSR, the latter already had MiG-25 and R-40 missiles; F-117 - even during the development it was quite clear that Soviet radars can easily track it (likely because it was based on the scientific research done by a Soviet scientist).
The F-35's "common platform" concept is of the same kind - looked amazing on paper but turned into a nightmare and limited the capabilities of all three variants. Moreover, it turned out that Lockheed didn't have and couldn't develop the vertical take-off design, so they had to invite Yakovlev's engineers who worked on Yak-141 to develop it and delegate the manufacturing to Rolls-Royce.
I know that Lockheed's "Skunk Works" is considered the most advanced engineering team but in my very humble opinion they are nothing more than a bunch of childish dreamers who are always trying to perform way beyond their engineering and technical abilities. Harsh?