I think the do it b/c they can. Sometimes, don't you ever switch your furniture around in your house? If the plans for the refurb DO NOT call for a particular detail, I would think that an imagineer would jump at the chance to make his/her mark on the park, even if that was a simple 180 turn of a set piece.
Sure there is plenty of room with no one around, add a few kids, who may have an issue with manners or waiting and it becomes a perfect reason why I dislike toon town so very much.
The same can be said about any area of the park. For example, Adventureland looks like it has plenty of room when there is no one around, add a few adults, who may have an issue with manners or waiting...
"Greetings, Starfighter! You have been recruited by the Star League to defend the Frontier against Xur and the Ko-Dan Armada."