Of course metadata is lost if not encoded anywhere on the way. The argument was made regarding code generation being more complex when code is saved on the intermediate level.
You're understating the problem a bit. There's no standard way to mark up C code as mapping back to the original source code so that metadata (source lines, memory mapping back to data structures) can be passed on to the compiled binaries. If the original language generated DWARF-encoded objects, then debuggers would just work, etc.
Yes, C was not designed to be intermediate compilation step and this yields losses of some information (e.g. debugging metadata, but also some semantics of source language may get lost). I never argued with that. I never said that this is a perfect setup that doesn't introduce any new problems. I just said that compiling to C is very close to what is actually happening inside the compiler targeting assembly from higher level language.
The techniques and difficulty in implementing the compiler itself are related but not really the same subject.