Looks like the only autoconf bit they use is an old copy of config.guess that was used in the LLVM they forked from (I think they've since taken it out entirely in the LLVM upstream).
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.
GPL doesn't care about inclusion or linking, it cares about derivative work. And somehow I doubt the 3d engine is derivative work of a piece of autoconf.
