I'd suss out the overall cost of porting the n54 head vs fitting a n53 head + manifold flange/s, and go from there. I think you would want cams in either case though, so consider the cost of that. If the appetite to spend real money (i.e. headwork + cams + engine build + new turbo setup) is there, you can't really go wrong with either option. Both flow a lot more than an untouched n54 head.
Doing the usual 600-800hp built n54 street car thing doesn't usually justify the cost/hassle of headwork in my view. While the head has well known shortcomings and making the n54 breathe better and feel more like a race engine is awesome, I don't believe fixing shortcomings with the head will add substantailly to the overall reliability of a built n54 engine, given the typical issues are usually found elsewhere (i.e. way too many shoddy people building/tuning n54's, cooling systems not adequate for intended use, factory di system, open deck block with insufficient cooling for the rear cylinders, etc). It is still a 15yo bmw engine that has suffered with issues and wasn't designed to make more than ~65hp/cyl.
But if you're in so deep on the build that you're willing to try make absolutely everything work better or more reliably, or you're chasing every ounce of potential, then you might as well. Lol.