We are in agreement. Your definition of system properties that do not derive simply from the sum of the elements is what the article is really talking about. That's closer to the physicist meaning.
models are taken (because there is no other way) as black boxes and the only comparison is made between the models not between a model and it's subsystems (because again noone knows the "sub-systems" of a model, those are just some derived weights that can not be ascribed any meaning). this is precisly the 2Mpx camera and the 12Mbpix camera comparison not the fluid dynamics vs particle movements comparison.