I took a tall 3.5 year old on the ride at California Adventure when he was 41" tall. It's the exact same ride system as Epcot.
No concerns with falling out, as others have noted. They have a loop for smaller guests.
If the height looks close, they might check 2-3 times. Be prepared for that because it can be annoying for you or the kid! The height thing is actually a little weird sometimes for them to put their feet right in the proper spot. It's actually amazing how the CM's just know if the height is close from looking. Our next trip to a Disney park the same kid was 45" tall. They didn't even think about checking him on Soarin' or any similar height rides like Big Thunder.
As for the ride, he loved Soarin'. The jumping whales and animals were a big treat for him!