I think that what's differnt in this case, is that Amy has a lot more negotiation skills available to use with Sheldon.. we know how she can use logic to convince him of things, and since he does see himself as an equal to Amy, she has a lot more possibilities on getting motions passed for modifications on the Relationship Agreement than Leonard with the Roomate Agreement.
And yes, like you guys said, I have seen arguments saying that this is a one sided relationship only on Amy's side
forgetting the fact that it was Sheldon who asked her to be his girlfriend and not the other way around, and it was Sheldon who spent first, Isolation Permutation worried and conforting Amy and then last episode totally jealous and stepping out of his confort zone out of jealousy... and nobody feels jealous that way if there are no feelings involved...