After further thought about this, I concluded that a much better idea is to just exclude fmgrprotos.h from the pgindent run. While renaming these two functions may or may not be worthwhile, it doesn't provide any sort of permanent fix for fmgrprotos.h, because new typedef conflicts could arise at any time. (The fact that the typedef list isn't fully under our control, thanks to contributions from system headers, makes this a bigger risk than it might appear.)
So I did that, and also added a README comment along the lines you suggested. regards, tom lane