Matt explained it already in the simple version. I.E. They flow better then the square port.
The other side of it is a long story. I'll touch on it.
Since the Hemi heads design was introduced (many, many yrs ago)it's been great on the intake and not so great on the exhaust. When you look at Intake to Exhaust CFM ratio. 70% or better exhaust to intake ratio has been a rule of thumb for as long as I can rememmber. The last place you want to remove material is on the short side. That just makes the port turbulant and flow less. So,,,you have to remove it else were. The D shape is proven and fit's nicely to the round header flange.(we first did it 3 yrs ago) Plus the fast moving air helps pull the intake charge in during valve overlap.
So for those that have round tube headers with the round flange. It's an option that doesn't cost anymore then the square port opening.
What are your thoughts on polishing the combustion chamber or the exhaust ports?