Because the fence was intended to prevent access for *everyone* whereas, with no fence, the train would only have been accessible to those without mobility issues. I see where they're going with their thinking, but I'm still not sure I understand why there would be major ADA complaints about it. Children (or adults, for that matter) who have mobility issues can still play in the area and enjoy the major intended feature--the "splash and soak" part. But in any case, I agree with WDW Magic that the best solution is to remove the steps leading to the engine and block the doorway into the engine.
This makes sense if they have no plans to let anyone in there. Someone over at WDW Magic had posted saying that a CM said that it would be open at certain times with a CM present to supervise. I normally don't put to much stock in CM rumors, but the whole front of the fence is a gate which lends credence to that report.