I've kept all my factory piping so far, the only issues I've had with it are the rubber seals.
I can't blame that on anything but age and high heat racing duty.
My rubber seals y to throttly body and on the front turbo are about shot.
You do no need to remove the engine to change any of the turbo piping I don't think.
There are several articles on here about others doing the same thing with piping.
There are several things that will get in the way to remove, but whole engine, for turbo piping, pretty sure no.
The rubber hoses that come off of the y pipe actually go to your side mount intercoolers.
The two hoses going into the y are charged with 1/2 boost at peak.
Air in, in&out the turbos, in&out the intercoolers, boost to the throttle body.
My pipes at the Y are showing signs of pressure, but have still not failed at 165k.
Silicone hoses seem to be popular, but oil and fuel quickly degrade them I've read.
Again, double check your ECU codes, caps, much more important than pipes/looks.
Sorry I can't be more helpful without owning or trying the parts your're asking about.
Hope I helped some, have a great day!