Alright, frustrated by the lack of support of Media Overlays in flowable EPUB 3 ebooks in iBooks, I wrote my own JS to emulate MO support on Apple's app.
I will release the JS soon with a complete example, I just need some time to polish the code a bit and add some init options.
Features (all at user's will) include:
2) assign CSS class to both active and paused SMIL element (possibly different, see the video)
3) a tap (or $n taps, with $n decided by the user) outside text fragments will pause/resume MO rendition or stop it and clear highlight
You can get the flavour from this video (apologies for the shaky hand): http://www.albertopettarin.it/misc/ttp.mp4