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This argument is definitely true for someone wanting to compile a kernely. To what extent, however, does this affect the generation of toolchains? In other words, does the toolchain, libc most likely, depend on specific CONFIG_* options, and if so, which?
There might be a few. Page size is set by config options on some arches, for instance.
Maybe it would be a good idea to start collecting such critical CONFIG switches on a per-arch basis, what do you think?
Sure. You might have a look at the couple of projects out there that are defining kernel headers outside the kernel tree just for things like glibc that need to know the kernel ABI. I think they're 2.6 only, but they might be handy for crosstool in the future.
For completeness, besides the linux/autoconf.h file a toolchain also requires linux/version.h. Obviously this is an arch invariant, though. In addition, the include/asm link is needed.
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