I think if you pay 200 dollars you get access to more builds and somehow code merging becomes possible, but I am not sure about that. I do know that is currently the only change I make every update, although I hate how it always sets my pixel perfect UI from point to trilinear filtering every time I update a texture. If I get the time to track that one down I might have 3 or 4 changes every build

It is annoying but it is better than taking the time to build my own system. I would rather make a pretty and functional UI and concentrate on gameplay. I can handle a certain level of "I wish that...".
Edit: I found the trilinear setting. NGUIEditorTools.cs in method MakeTextureAnAtlas (string,bool) comment out the
settings.filterMode = FilterMode.Trilinear;
and now whatever you set the atlas texture filter mode to will not change when you add/update a texture!