line from mechanical pump is to keep fuel contained in the case of a diaphragm rupture. If the hose is routed to a vacuum source, it will indeed collapse. My lines (carb motors) are routed above the throttle plates (not a vacuum source). Wouldn't think your hoses are an issue.
You mentioned the noise takes a couple of seconds to go away at shutoff. If the noise continues after all rotation has stopped, then it will not turn out to be gear noise, or any other driveline noise. Belt noise can continue until the rotation is completely stopped, but not afterwards.
You have a high pressure regulator on the fuel rail(s) that bypasses fuel back to the high pressure pump. Get a stethescope and rule out that puppy before you start spending money.