It's a fair question; since not every single part of the car is
built by the manufacturer themselves.
E.g Nissin brakes, IHI turbos, Garrett turbos, recaro seats, momo
parts...
Engine development is quite unique to each manufacturer (except
some of the one-off supercar types that use BMW or Merc engines),
but I believe not every single component is manufactured by their
own factories.
On paper, the new skyline is around 400 bhp or so right? Don't
really remember... whereas the R34 GTR was supposedly 320bhp in
stock form. So stock to stock, theoretically the new one is more
powerful.
The RB26DETT has proven to be able to handle high horsepower even
in stock form though, and I'm not sure if you want to compare mod
potential, which engine would win.