Randomly discovered this when checking a card for previous footage before a format. I had used it in a GH2 with the "Apocalypse Now" hack and the C100 was able to play all the clips.
If I put a card formatted and shot by an FS100, it turns up in the C100 absolutely fine. FCPX sees both and really doesn't care.
It's a double-edged sword - we get cross-compatibility, but at the expense of flexibility.
We can't mix frame rates on a card. We can't have unique file names on a card.
But I notice that it takes longer to read a Canon AVCHD card vs an FS100 AVCHD card in my NLEs. I think this is more to do with the fact that Sony seeded its structure and applied a little 'Cosa Nostra' love in the same way that it seeded its v1.3 HDMI Time Code (Canon chose to fete only Atomos).