Of course that's a different proposition than e.g. compiling a C program to LLVM IR using Clang and then trying to compile that IR on a different target, or trying to interact with non-LLVM-IR functions that conform to the platform ABI.
Of course, the resulting native code may not be the best for the target, since e.g. a native integer on one platform might become a pair of smaller integers on another platform. But it could work.
With all of that said, I expect the proposal was to use the Rust compiler to compile the Rust compiler to IR, and I imagine Rust is complex enough that it must generate at least some target-specific IR. Perhaps one could take the generated IR and "normalize" it, but it's questionable whether it would be worth it.
Of course anything compiled on x64 failed to link on ARM.
For an example, look at http://llvm.org/devmtg/2014-10/Slides/Skip%20the%20FFI.pdf, from page 103 to 107.
Edit: There seems to be a misunderstanding. What I am saying is that "LLVM IR is mostly architecture indepedent" is false. LLVM IR is not even remotely architecture independent and nonportability happens with even the simplest codes.