To start off with this seemed like a fruitless quest however I eventually found a relatively new project called Cog
It's technically possible to convert FLAC into Ogg-FLAC without re-encoding but there doesn't seem to be a utility to do it. Any ideas?
the libflac tools have a command-line switch (if you weren't familiar with it), which allows you to wrap flac file inside an Ogg container. I don't know if it could be done without re-encoding, my guess would be no, writing FLAC files into an Ogg container is an extra step, in much the same way Vorbis packets are written into an Ogg container.