Reorder protobuf compiler command line arguments.
Attempt to chase non-repoducible bug. CL crrev.com/2239383002 has
changed a command line for protoc and there are rare occasional
crashes on Win32. It could be because of some bug in protoc's parser.
This change restores a command line like before the suspecting CL
only for the most common case with only one proto file in a library.