Just bouncing an idea around for you, I am not 100% sure why it is happening, but externally that just looks to me like you have pressure of 0~1 bar in most of it because that is atmospheric pressure. It has to show it on the scale, I don't think it looks crazy.
Where as your internal simulation while it has an outlet, doesn't have variables determining the pressure etc. if you changed your l/min to atmospheric pressure then the pipe would probably look the same in both simulations. Then you can set surface goals at the outlets and read off the exact pressure there and the volume flow.
Can anyone place help?