If the MP4 is "fast start" the index is at the beginning so you can "stream" it.
I suspect scene standardization on MKV would probably encourage Apple and Sony to deliberately not support MKV (instead of not supporting it out of laziness, as they currently are).
When DivX made their H264 codec, DivX 7, they actually chose the matroska container. Of course, DivX has lost a lot of the brand name recognition they once had (their logo used to be on nearly every DVD player), so the penetration of matroska in this respect isn't that high. There is also WebM, of which the container uses part of matroska, which might help penetration (of course, its people like Apple and Sony who aren't likely to implement WebM).
Other then that, only a few embedded products support mkv (TVs, set top boxes). These are pretty much impossible to update, so it is pretty much impossible to recommend matroska at this point, since a large amount of people would watch these videos on such products.
I suspect scene standardization on MKV would probably encourage Apple and Sony to deliberately not support MKV (instead of not supporting it out of laziness, as they currently are).