That's to become the right way of "fixing" it.
Since in the recent versions of the builder I now use the "official" Win64 builds of LLVM and Clang (which include the LLVM Mach-O linker), and no longer my own branch of them, the only thing I can do (apart from re-creating a new LLVM branch and managing the LLVM builds myself again) is to open a ticket on the official LLVM GitHub. But I'll tell you it would have 80-90% chances of being rejected, because actually that's *not* a bug in the LLVM linker. It's just that -Wl,xxx is not a linker flag, so it shouldn't appear in a project's *linker* flags ; and the Apple linker just "tolerates" it.
The Right Thing To Do(tm) would be to get rid of these flags in the project files themselves (either in the main Xcode project file, or in the files pulled from outer space by CocoaPods), by replacing every occurence of "-Wl,<something>" with just "<something>" in all possible variants of the linker flags. And if these occurrences come from a Pod, contact the Pod maintainer and tell him that he's got a little thing to fix.
... or, just use the Apple linker. The LLVM one has not yet completely replaced it.