no and yes.
no, you can't use animate canvas video like you can with as3 video and add the video to the timeline, create a layer(s) above the video and add new content.
yes, you can add content above html5 video outside animate.
You're saying to use other software for this? I know Captivate has some of this capability of interactive video and within the spectrum of interactive video software, there is a huge $$ range and that Captivate is at the bottom, bare bones minimum. I saw that some software is $300 / month. Some $30,000 a year.
i would edit the js file (or add a 2nd js file) and edit using a text editor. but there might be software that makes this easier.