Spent some weekend time on this and got both chunked streaming for Safari and a bisection-based seek working[1]. Haven't merged it into the TMH version yet as I'm not satisfied with the seek performance, but I have a pretty good idea how to seek based on Ogg Skeleton metadata by using liboggz on the C side and giving it custom i/o functions that manipulate the JS XHR wrapper.
Of course, now I need to redesign the controls for the mobile overlay so there's a way to actually invoke the seeking. ;) (On desktop it should be able to use the existing controls in MwEmbedPlayer.)
Yes using the ogg index would be the way to go, bisection seeking never worked too well for native implementations either. All derivatives created in WMF should include ogg skeleton / index.