@THD+N
I can now see that the simulation is based on the measured CLIO data shown above: Fs 32.08 Hz, Qts 0.24 and Vas 268 litres. Those figures are quite different from the rough working values I had been using, particularly Fs and Vas, and that seems to explain why the higher tuning produces a much flatter alignment.
My provisional figures came from averaging measurements of four different 414A woofers, which gave approximately Fs 26.6 Hz, Qts 0.226 and Vas 150 litres. I realise that averaging four vintage drivers is not the same as measuring my own pair, and it also appears that individual 414As may vary quite considerably. I will therefore regard any simulation as provisional until I can measure my own drivers.
Your explanation of the response curves also makes sense to me. The 53 Hz tuning clearly gives the flatter fourth-order alignment and the lower formal F3, whereas the 39 Hz tuning retains somewhat more output below approximately 45 Hz but introduces a gradual downward slope through the upper-bass region.
This makes Bobland’s quick-swappable ports seem particularly useful. It should be possible to begin with the 6-inch tubes, compare them with slightly shorter alternatives, and then confirm the actual tuning with an impedance sweep and listening in the room.