That's a completely different program. GPL doesn't jump across programs.
There's actually a carveout in config.guess's license that lets you redistribute it under whatever license you want but only if you're actually using an autoconf-based build. The LLVM version this is based off of only uses config.guess and not anything else from autoconf, so that carveout doesn't apply. Instead LLVM just relied on the fact that config.guess is only getting called via the command line, so the GPL's "virality" doesn't apply; LLVM (and now Microsoft) just distributed config.guess separately licensed as GPL alongside their code.