Can't test it now, if it will work on the Android, as my connection here atm is to bad to stream any video at all and Youtube app does seem to make some problems (always get a can't playback this video message).
However, on the youtube webpage, the following link will enable to link to a specific part of a video.
http://www.youtube.com/watch?v=1aBaX9GPSaQ#t=1m02s (1 minute, 02 seconds)
Since the Youtube App should work in a similar way (i.e. catch intents which are directed to youtube.com domain and with a path of /watch), there is a good chance it will take the anchor (#t=1m02s) and correctly jump to that mark.