Not to be pedantic but it may depend on what you mean by better flow.
The steady state mass flow rate for a given pressure is likely to be higher for the larger orifice, just because of the first pass restrictions in series analysis. (For a system with gas velocities this high and viscosities this low, you're basically always turbulent). The old 32º Magnaflow valve did in fact produce an increase in velocity, all other things being equal.
I concur that the smaller port probably will suffer less energetic losses per unit gas flowed to the ball. This would manifest as better efficiency at the same velocity, albeit at a higher pressure to normalize overall energy flows.
Also concur that port matching is the best policy. it's a little trickier at the bolt because of machining and such, but the Hardshell Intimidator bolt was my favorite implementation of a stacked tube bolt, since the rear could be 3D machined to a "perfect" flow path..
Steve and I have kicked around the idea of a resurrection spec control freak valve w/ an angled and matched air path just because I'm so horrified by the Alien morph valve.