Chapter markers do not show up in Quicktime videos on iOS since iOS 6 was released (outside of videos purchased from Apple).
You can update channel entries in ExpressionEngine using DataGrab Pro, but you must have a unique identifier field outside of the actual ID. Using the title field as the reference for detecting an existing entry works, but if your titles include quotes it's easy for a mismatch to occur.
There are several HTML5 video players available, but not all support playing YouTube videos. Sublime Video does.
To play a video at a specific time, use the Sublime Video player.seekTo() api call.