Things like cameras (gameplay, replay and exterior), police officers, net color, pitch mow pattern are linked to DB stadium IDs (the two last are editable from the App). I am not 100% sure for atmosphere, but I see no reason why it would not be the case. At least I didn't notice anything weird in that regard while using the App.
Yes no reason why it wouldn't use the original atmosphere, thats great because it would also mean that the cameras would be the ones of the original stadium. Sometimes with stadium server the camera was into the stands, as the cameras of two big stadium used as default id's wouldn't match to the stadium with stands close to the pitch.