Ah, I relate to the questions gone unanswered thing so I had to respond . Though I don't know the answer to the photopass question so I am not super helpful. Perhaps shoot the PP folks an email at wdw.photo.imaging@disneyworld.com? They are also on Facebook.
The boats run until approximately 45 minutes after the park closes unless the schedule has changed fairly recently. I have caught it a bit later than that, by pure luck, but I wouldn't push it.
So, on PM EMH nights, they will still run during EMH hours? The night I am planning to use them, we want to watch EWP and Wishes from Poly beach, then use the boats to attend EMH hours from 11pm - 1am.
Our favorite place to watch fireworks is over on a small beachside hill near the Tahiti longhouse which is pretty near the TTC ferry. It might be an alternate idea just planning to head over there where you know you can catch the ferry? I have only taken the monorail when heading to PM EMHs though, sorry, OP.