why doesnt it make sense for a natural system? What do you expect a natural system to look like? As far as I can imagine, a universe that can be observed must display some consistent sent of mathematical rules (because any universe that did not, would be too chaotic to allow an ordered system like life to exist within it, and therefore all observers will find themselves existing within the limited ones), and a simulation is itself just executing a bunch of mathematical rules, and so any universe you can exist in will appear indistinguishable from a simulated one from the inside (unless the simulators do something specifically to reveal it).
I would think of life as being ordered, yes. complicated, and with components small enough that we have a hard time envisioning it, but its not really much different from what you would get if you made a bunch of microscopic robots able to assemble more of themselves, and had them stick together to form a larger structure. We would probably imagine such things be made of something other than water and carbon chemistry, because when we make machines we usually use metal and silicon, but at the scale of cells where a component can be an individual molecule, carbon chemistry works well. I just think that we have poor intuition for what chaotic and ordered systems look like if the scale is beyond what we can see unaided.