I'm sure the FSF sees this as a tradeoff that has to be made in order to keep free software viable. But that's a very different story than "user freedom is everything".
It is certainly fair in the sense that the Linux or BSD kernel people will never get to see, and benefit from the NT code, but microsoft and Apple can certainly use any BSD or MIT licensed code they want to.
But using Linux kernel code in the NT kernel is a special case of software sharing that can only be done at the source code level, by experienced programmers. And then it has to be released by the project maintainers, in this case the linux foundation, or microsoft.
But application code (e.g. an mp3 player), can be released for both windows and linux whether they are closed-source, or GPL.
The kernel might not be the best example to make your point.
That presumes that the FSF's tradeoff is getting things wrong. If this strategy is what results in maximum overall user freedom, then that is exactly the strategy you have to follow if "user freedom is everything".
It is meaningless to say that making slavery illegal is a tradeoff that has to be made in order to keep a free society viable, but that is a very different story than "human freedom is everything". Yes, human freedom is everything, and that is exactly why we restrict people from owning slaves, there is no contradiction there.
This is not inconsistent with "user freedom is everything".