Ignoring for a moment that this is expressly permitted, it seems like the concern is this:
The kernel provides two de-facto outputs: (1) a GPL-covered kernel, and (2) "Headers for libc implementations".
From a commercial standpoint this is akin to a free version and paid release (or a dual-licensed release). That one is generated by "just a script" is immaterial. What's relevant is that two independent artifacts are created.
Now, Google, instead of using the official "Headers for libc" wrote their own script. This script could have been 'cat' or anything else - what is material is that the copyright notices are stripped. Normally, I think everyone agrees that it is wrong to strip the copyright from a file whether it's a C file, an H file, or GPL-licensed documentation.
So: wouldn't it be easier to update the "official" script, bundled with the kernel sources, to replace the copyright notice in the generated headers with an express lack of copyright notice? If these headers are not GPL covered, clearly they shouldn't say that they are. Right?