Seems like a good opportunity lost to wow riders when the train holds. I would think an easy (and I mean easy) fix would be just to add more yeti shadow projection in the event this happens. Perhaps have the Yeti run back across the track, "see" the riders, do a king kong style chest beat, before swinging off again. Anything to fill the void of nothingness while waiting... The hold up at show scenes really impact story continuity. Haunted Mansion counteracts this in effect by having tons of visual stimuli to keep us happy. Not to mention a perfect audio spiel for when something like this does occur.
I think the imagineers working EE realized this issue at the initial track switch and thusly added the bird on a stick to keep riders "entertained" during the unfortunately slow track switch. Same could be done during the projected scene. But that's just my idea.