While I work for Google, and was involved in the CPTN and Rockstar stuff (and thus can't comment on this article at all, though I wish I could), i can actually point out that this statement is not right.
First, companies that wish to contribute to LLVM are asked to non-assert patents involved in their contributions. This is covered in the dev policy, and has been for a long time. Their are non-assertions/grants on file for a number of companies now.
As for whether Apple owns any patents on LLVM core, Chris Lattner himself told me Apple held none, which is why they had not filed a non-assertion.
Apple may or may not hold patents on LLVM code that is not "in tree" (so yes, they may have non-public frontends or backends they own patents on), and I never specifically asked about the clang frontend, but I trust Chris enough to know that if there was in-project code, be it clang or core or whatever, he would have followed the dev policy and Apple would have non-asserted them.