Over time the hoses start to deteriorate and can start coming apart inside. Several have experienced this to the point where they couldn't even hold rail with a lift pump because pieces were coming off like a flap sort of restricting flow. Plus depending on how many years you ran without filters between the tank and your stock filter and the quality of the fuel you run, a build up like a scale can happen that over time which starts to come off over time. I've seen it inside of the hard lines on my own truck.
My point is that in a common rail fuel system, cleanliness is key. Many claim they have never had a problem so it's ok, but you are rolling the dice. There is a reason EVERY diesel has the filter close to the engine.
They way I see it, as long as at the CP3 you see a good positive pressure from the lift pump and at your max PW rail pressure also holds then run the filter. Even if you need 20psi at the pump to get 10psi at the cp3.