Unless it's a PCS-specific thing, all three quad-cores available do have the HD4000 - at least as far as Intel's site is concerned, though it does warn that: "Graphics may not be available on all computing systems. Please reference the system, motherboard or chipset specifications for compatibility."
So the compatibility may change between laptop models.
I'd like to know for sure myself, since I plan on picking up an Optimus/Vortex with one of the quads.
Yamikotai, my Optimus III uses an i7-3610QM (quad core) and it uses an Intel HD 4000 integrated graphics card (as well as the GT 650m).
edit: it might be an error in the configurator, the advice to update to a nvidia GPU doesn't make sense on the Xenon II as there is no discrete GPU option. i'd give PCS a ring/email to make sure