Well, after some quick testing with some random MKV files I had kicking around...
Exact copy of the original yielded 100% efficiency.
Remuxing (removing chapter markers) resulted in ~99% efficiency.
Remuxing (removed audio track) resulted in ~8% efficiency.
So it appears that the audio and video streams are indeed interleaved in MKV, enough so that block level de-dup doesn't do much for them.
I haven't tried with MP4 or M2TS but I suspect the results will be similar. But it will have to wait until tomorrow because I'm tired and I'm going to bed.
I think I'll also check between containers to see how will that works with the block level de-dup. Since the streams in the containers are the same I wonder how much of the data will be shared differing containers.
RAID protection is only for failed drives. That's it. It's no replacement for a proper backup.