Seems to me that since the Transportation is for RESORT guests (mostly) and that EMH is for RESORT guests only, that the time would still be a half an hour before opening for Resort guests. Thus if there is EMH then it would be 30 minutes prior to that time.
That being said, we don't generally do the morning EMH so this has never been an issue for us. The only thing we have done in the past is had an early morning reservation for breakfast (CRT) before the park officially opened. We did nothing special except take the normal boat over. Worked our way to the front and into the park. (Very magical to walk down main street with virtually NOBODY around to photo bomb the pictures). We made it with plenty of time to spare. This was about 4 years ago. In all honesty, I don't recall the times. I just recall asking what time we could get the boat to make the reservations.