I don't think Toyota wouldn't go to the extra cost of putting in a spacer there, I reckon they would make the mounts longer if that was the case. ( I could be wrong though)
I think it is to protect the mounts from oil and dirt etc (rubber doesn't like mineral oil which comes out of the engine pretty regularly)...

Sam if you have allowed it to stay on there I dont think there will be a problem, if it helps your mounts last a bit longer then that is a good thing.

Jonny, that's interesting, how are the two plates different?