Within very generous tolerances, humans are insensitive to phase shifts.
He also points out that in a normal room sound is reflected many times
from objects at multiple distances resulting in enormous amounts of
phase shifts that dwarf the far smaller phase shifts in amplifiers (a
lot of this read like Duke's take on this)
This is entirely correct; you can't sense phase at all if you're talking about a single frequency like a sine wave.
But leaving sound stage information aside (which might be messed with due to reflections) phase shift over a spectrum is perceived as a **coloration**, for example a rolloff above the audio band can be heard as a darkness in the highs if the rolloff is close enough to the audio band. In the bass its a similar phenomena, if rolling off prematurely (above 2Hz) even though your speakers are flat to 20 Hz it will be perceived as a lack of impact.
Because speakers are mechanical devices, a rolloff in them does not cause this problem.
I first became aware of how profoundly this was true a long time ago when trying to find out why an MFA Magus preamp sounded bright in the phono section. A dealer of mine wanted to sell the preamp instead of a competitor's but the brightness made it as bad as poor digitial of the day. I investigated the circuit and found that at 50KHz the circuit went from the RIAA equalization curve to flat. I removed the components responsible and the brightness was eliminated, with no sense of darkness- LPs sounded just fine after that. Now you'd think that at 50KHz there wouldn't be an issue, but phase shift can extend down to about 10th the frequency where this was happening (5KHz) so its easy to see how this was heard as a brightness. This principle is easy to demonstrate.
I can put this another way: there is a **reason** that Jensen feels they needed to go so low (1Hz) with their subwoofer transformers. Jensen transformers are extremely well designed, are high quality, and the designer is held in high regard in home and professional audio. Anecdotally, I've tried using regular full range audio transformers made by Jensen for subwoofers and while they work OK, you can easily hear that something isn't right about the bottom octave- which is fixed using the Jensen subwoofer transformer. Preventing phase shift is is also why Stuart Hegeman of Harmon Kardon Citation fame insisted on wide bandwidth in his designs.
Since you already have the transformers I would go ahead and use them. But I would also get the subwoofer transformers and then audition them side by side- see what you think.