1st one is probably because of a boost gauge as you rightly said. normally the pipe goes directly from the throttle body to the map sensor with nothing in between.
tha bypassed valve can be removed if you like? not sure exactly which one it is, but i think its to do with the idle up control when the air con is on. if the car runs fine i wouldnt worry.
the final one is a pipe that would normally come from the standard actuator to the high/low solenoid. if you have an aftermarket/adjustable actuator then many people dont use the high/low function anyway.