You lose a lot of things the C compiler does for you by targeting LLVM directly. A big one is debug info. The C compiler will emit debug information for you, and with some line directives, as shown in the article, or maybe scripts, you can get minimally usable source-level debugging without having to generate your own debug info.
LLVM has high-level support for debug info. (You have to actually generate it, which isn't free, but neither is generating #line directives, so it's arguably a wash.)
