The secret is to count frames and create cues that stop the file at each point when the transition stops. Using a Hog 3, I'll build the main cue to Setup as an InFrame on one list. Then I create a second list with Play modes setup as follows:
im going to try and create a playmode that does this automatically. ( when i get time )
after peeking around it seems keynote does dump frame information for the slides into quicktime chapter tracks - as part of the movie export.