I have not ported any of my TDI engines. Do they 'breathe well enough'? Sure. Would 4 valves per cylinder increase their ability to breathe well? Absolutely. I do not think starting with a gasser head would make for less work. I am not thinking of mixing and matching heads/blocks. I would use the full CR longblock, bolt on the ALH pump bracket where the high pressure CR pump is, fit a custom intake and injection lines and modify the head/injectors to fit.
Standalone electronic VNT control will be completed before putting any serious consideration into an mTDI CR engine.